Virus-Receptor Interactions: The Key to Cellular Invasion

Distinctive function of Tetraspanins: Implication in viral infections

Harboring four transmembrane domains in their structural hallmark, Tetraspanins (Tspans) are a family of glycoproteins with pivotal functions in a variety of biological and cellular processes. Through interacting laterally with each other or specific membrane proteins, Tspans organize tetraspanin-enriched microdomains (TEMs), modulating cellular signaling, adhesion, fusion, and proliferation. An abundance of evidence has identified the multiple functions in the progression of cancer as well as the underlying molecular mechanisms. Recently, plenty of studies have focused on the utilities of Tspans by pathogens for infection, especially the infection of viruses. The expression of Tspans correlates with the phase of viral infection, the type of virus, and targeted therapies. In particular, perturbations of Tspans in host cells can affect viral attachment, intracellular trafficking, translation, virus assembly, and release. In this review, we summarize and provide a historical overview of the discovery and characterization of various kinds of virus infection and highlight their diversity and complexity, along with the virus life cycle. Furthermore, we examined the current understanding of how various Tspans are involved in the regulatory mechanisms underlying viral infection. This review aims to offer a comprehensive understanding of the targeting of Tspans for therapeutic intervention in infections caused by diverse pathogens.

Predicting and preventing the next viral disease transmitted through food

The ability of viruses to infect humans following oral exposure and disrupt normal physiological or anatomical functions is a hallmark of their potential to cause foodborne disease. While the etiology of the vast majority of foodborne diseases remains undetermined, viruses are often identified as the culprit when the cause is ascertained. Many undiagnosed causes of foodborne illnesses, especially sporadic cases, may go undetected or be caused by yet-to-be-identified viruses. The potential for food to become a transmission vehicle for viral diseases that are not typically acquired following ingestion may be described within the epidemiological paradigm. This model considers the characteristics and interactions of the host (the human), the agent (the virus), and the environment (the food, the food producing animal or the food production environment). Importantly, these factors are not static and evolution of viruses, transformations in agrifood systems, and changes in environmental conditions and human health and behaviour may contribute to increased pathogenicity, virulence, or exposure. In the context of determining the potential for additional viruses to emerge as important causes of foodborne disease, factors that contribute to hazard characterization (e.g., receptor affinity and distribution) and exposure assessment (e.g., prevalence in food animals and food hygiene) are reviewed. Although it is not possible to predict the type, the timing nor the location of the emergence of the next important cause of foodborne viral disease, the deployment and implementation of actions and behaviours related to personal and food hygiene, sanitation, and safe food handling practices can reduce the likelihood and impact of known and emergent viruses on the safety of the food supply and human health.

IgStrand: A universal residue numbering scheme for the immunoglobulin-fold (Ig-fold) to study Ig-proteomes and Ig-interactomes

The Immunoglobulin fold (Ig-fold) is found in proteins from all domains of life and represents the most populous fold in the human genome, with current estimates ranging from 2 to 3% of protein coding regions. That proportion is much higher in the surfaceome where Ig and Ig-like domains orchestrate cell-cell recognition, adhesion and signaling. The ability of Ig-domains to reliably fold and self-assemble through highly specific interfaces represents a remarkable property of these domains, making them key elements of molecular interaction systems: the immune system, the nervous system, the vascular system and the muscular system. We define a universal residue numbering scheme, common to all domains sharing the Ig-fold in order to study the wide spectrum of Ig-domain variants constituting the Ig-proteome and Ig-Ig interactomes at the heart of these systems. The "IgStrand numbering scheme" enables the identification of Ig structural proteomes and interactomes in and between any species, and comparative structural, functional, and evolutionary analyses. We review how Ig-domains are classified today as topological and structural variants and highlight the "Ig-fold irreducible structural signature" shared by all of them. The IgStrand numbering scheme lays the foundation for the systematic annotation of structural proteomes by detecting and accurately labeling Ig-, Ig-like and Ig-extended domains in proteins, which are poorly annotated in current databases and opens the door to accurate machine learning. Importantly, it sheds light on the robust Ig protein folding algorithm used by nature to form beta sandwich supersecondary structures. The numbering scheme powers an algorithm implemented in the interactive structural analysis software iCn3D to systematically recognize Ig-domains, annotate them and perform detailed analyses comparing any domain sharing the Ig-fold in sequence, topology and structure, regardless of their diverse topologies or origin. The scheme provides a robust fold detection and labeling mechanism that reveals unsuspected structural homologies among protein structures beyond currently identified Ig- and Ig-like domain variants. Indeed, multiple folds classified independently contain a common structural signature, in particular jelly-rolls. Examples of folds that harbor an "Ig-extended" architecture are given. Applications in protein engineering around the Ig-architecture are straightforward based on the universal numbering.

Mutations Inactivating Biosynthesis of Dispensable Carbohydrate-Antigens Prevented Extinctions in Primate/Human Lineage Evolution

The human natural anti-carbohydrate antibodies anti-Gal, anti-Neu5Gc, and anti-Forssman are "living-fossils" that appeared in ancestral apes, monkeys and hominins millions of years ago. These antibodies appeared at various evolutionary periods in few mutated-offspring that lost the ability to synthesize the corresponding dispensable (i.e., nonessential) carbohydrate-antigens, α-gal epitope, Neu5Gc (N-glycolyl neuraminic acid) and Forssman-antigen, respectively. Production of these antibodies is stimulated by environmental antigens such as those of the human microbiota. Elimination of carbohydrate-antigens in the few mutated-offspring was caused by accidental nonsense or missense mutations that inactivated genes encoding enzymes involved in their biosynthesis, while most individuals in parental-populations continued synthesizing these carbohydrate-antigens. It has been suggested that dispensable carbohydrate-antigens which are absent in some mammalian species were evolutionary eliminated due to selective pressure by lethal viruses using these carbohydrate-antigens as "docking" receptors. An alternative selective mechanism which is based on the distribution of anti-Gal, anti-Neu5Gc and anti-Forssman in mammals, is presented in this review and is associated with the protective effects of these natural antibodies. It is suggested that epidemics of lethal enveloped-viruses caused the extinction of parental-populations synthesizing the corresponding carbohydrate-antigens of these antibodies,  independent of the cell adhesion mechanisms of such viruses. However, the few mutated offspring were protected by these natural antibodies which bound to carbohydrate-antigens synthesized on viruses as a result of their replication in individuals of the parental-populations. Recent studies suggest that these antibodies continue to contribute to the immune protection of humans against zoonotic infections by viruses presenting α-gal, Neu5Gc or Forssman antigens.

The HAVCR1-centric host factor network drives Zika virus vertical transmission

Zika virus (ZIKV) vertical transmission results in devastating congenital malformations and pregnancy complications; however, the specific receptor and host factors facilitating ZIKV maternal-fetal transmission remain elusive. Here, we employ a genome-wide CRISPR screening and identify multiple placenta-intrinsic factors modulating ZIKV infection. Our study unveils that hepatitis A virus cellular receptor 1 (HAVCR1) serves as a primary receptor governing ZIKV entry in placental trophoblasts. The GATA3-HAVCR1 axis regulates heterogeneous cell tropism in the placenta. Notably, placenta-specific Havcr1 deletion in mice significantly impairs ZIKV transplacental transmission and associated adverse pregnancy outcomes. Mechanistically, the immunoglobulin variable-like domain of HAVCR1 binds to ZIKV via domain III of envelope protein and virion-associated phosphatidylserine. Proteomic profiling and function analyses reveal that AP2S1 cooperates with HAVCR1 for ZIKV internalization through clathrin-mediated endocytosis. Overall, our work underscores the pivotal role of HAVCR1 in mediating ZIKV vertical transmission and highlights a therapeutic target for alleviating congenital Zika syndrome.

Computational insights into host-pathogen protein interactions: unveiling penaeid shrimp and white spot syndrome virus interplay

White spot syndrome virus (WSSV) has been a major threat in shrimp farming system especially for penaeid shrimps. The lack of effective control measures for WSSV makes this disease a significant threat to aquaculture. This study seeks to explore the mechanisms of WSSV infection and its impact on shrimp by examining host-pathogen interactions (HPI) through in silico approach, which can offer valuable insights into the processes of infection and disease progression. The investigation focused on five Penaeus species, including Penaeus vannamei, Penaeus chinensis, Penaeus monodon, Penaeus japonicus, and Penaeus indicus, studying their interaction with the WSSV. This study employed orthology-based and domain-driven analyses to reveal protein-protein interactions (PPIs) between the host and the pathogen. The combined strategies were found to be effective in detecting shared molecular mechanisms in pathogenesis, unveiling intricate PPI networks critical for virulence and host response. Most interacting proteins in WSSV are immediate early proteins involved in DNA replication and proliferation, and are crucial for ubiquitination, transcription regulation, and nucleotide metabolism. A large number of host proteins interact with WSSV across species (2360-11,704 interactions), with P. chinensis (11,704) and P. japonicus (11,458) exhibiting the highest counts, suggesting greater susceptibility or response. Host hub proteins are crucial in signaling, cellular processes, and metabolism, interacting across the cytoplasm, nucleus, and membrane, highlighting their role in WSSV pathogenesis. This study provides essential insights into host-pathogen interactions, offering a foundation for future research aimed at improving WSSV control in shrimp aquaculture.

Cell surface heparan sulfate is an attachment receptor for grass carp reovirus

Grass carp reovirus (GCRV) causes hemorrhagic disease in grass carp, leading to significant economic losses in China's aquaculture. However, the cellular receptors responsible for the initiation of GCRV infection remain unclear. This study reveals that cell surface heparan sulfate (HS) acts as a crucial attachment receptor for GCRV. Removing HS with heparinase significantly reduces GCRV attachment and infection. Both HS and its homologue, heparin, inhibit the attachment of GCRV to cells. Altering HS levels in cells affects GCRV attachment and infection accordingly. GCRV outer capsid proteins VP5, VP56, and VP35, as well as purified GCRV virions, directly bind to HS. Pretreating GCRV with heparin or feeding grass carp with feed containing heparin significantly reduces mortality caused by GCRV infection. Collectively, these results highlight the crucial role of HS as an attachment receptor for GCRV and therefore provide a promising target for the prevention and control of this virus.

The Na+-K+-ATPase alpha subunit is an entry receptor for white spot syndrome virus

White spot syndrome virus (WSSV) is a debilitating viral pathogen that poses a significant threat to the global crustacean farming industry. It has a wide host tropism because it uses several receptors to facilitate its attachment and entry. Thus far, not all the receptors have been identified. Here, we employed a BioID-based screening method to identify the Na+-K+-ATPase alpha subunit (PvATP1A) as a potential receptor in Penaeus vannamei. Although during the early stages of WSSV infection, PvATP1A was induced and underwent oligomerization, clustering, and internalization, knockdown of PvATP1A inhibited viral entry and replication. PvATP1A interacted with the WSSV envelope protein VP28 through its multiple extracellular regions, whereas synthetic PvATP1A extracellular region peptides blocked WSSV entry and replication. We showed that PvATP1A did not affect WSSV attachment but facilitated internalization via caveolin-mediated endocytosis and macropinocytosis. These findings provide a robust receptor screening approach that identified PvATP1A as an entry receptor for WSSV, presenting a novel target for the development of anti-WSSV therapeutics.

IMPORTANCE

Cell surface receptors are crucial for mediating virus entry into host cells. Identification and characterization of virus receptors are fundamental yet challenging aspects of virology research. In this study, a BioID-based screening method was employed to identify the Na+-K+-ATPase alpha subunit (PvATP1A) as a potential receptor for white spot syndrome virus (WSSV) in the shrimp Penaeus vannamei. We demonstrated that PvATP1A interacted with the WSSV envelope protein VP28 via its multiple extracellular regions, thereby promoting viral internalization through caveolin-mediated endocytosis and macropinocytosis. Importantly, compared with previously identified WSSV receptors such as β-integrin, glucose transporter 1 (Glut1), and polymeric immunoglobulin receptor (pIgR), PvATP1A demonstrated significantly enhanced viral entry, indicating that PvATP1A is a crucial entry receptor of WSSV. This study not only presents a robust approach for screening virus receptors but also identifies PvATP1A as a promising target for the development of anti-WSSV therapeutics.

Conserved spike protein in Avastroviruses: A potential factor in cross-species transmission

Avastroviruses (AAstVs) are important pathogens in avian species, with cross-species transmission being a critical factor in their evolutionary dynamics. The spike protein encoded by the ORF2 region plays a central role in viral entry and is believed to influence host range and transmission across species. This study analyzed the evolutionary conservation and divergence of spike proteins across different AAstV strains. Using sequence alignments, structural predictions via AlphaFold 2, and protein structure comparisons, we found significant structural conservation, particularly in β-sheet regions, despite originating from different hosts. Ancestral state reconstruction using BEAST 2.7 traced AAstVs back to a common ancestor from around 780 AD, with host-jumping events contributing to the formation of distinct viral groups. The conserved spike protein structures support the hypothesis that spike similarity plays a crucial role in cross-species transmission. Our findings highlight the crucial role of spike protein conservation in enabling AAstV to infect multiple host species, providing insights into the molecular mechanisms of host adaptation and viral evolution, and future studies will aim to experimentally validate the role of spike proteins in cross-species transmission.

It's a Small World After All: The Remarkable but Overlooked Diversity of Venomous Organisms, with Candidates Among Plants, Fungi, Protists, Bacteria, and Viruses

Numerous organisms, including animals, plants, fungi, protists, and bacteria, rely on toxins to meet their needs. Biological toxins have been classified into three groups: poisons transferred passively without a delivery mechanism; toxungens delivered to the body surface without an accompanying wound; and venoms conveyed to internal tissues via the creation of a wound. The distinctions highlight the evolutionary pathways by which toxins acquire specialized functions. Heretofore, the term venom has been largely restricted to animals. However, careful consideration reveals a surprising diversity of organisms that deploy toxic secretions via strategies remarkably analogous to those of venomous animals. Numerous plants inject toxins and pathogenic microorganisms into animals through stinging trichomes, thorns, spines, prickles, raphides, and silica needles. Some plants protect themselves via ants as venomous symbionts. Certain fungi deliver toxins via hyphae into infected hosts for nutritional and/or defensive purposes. Fungi can possess penetration structures, sometimes independent of the hyphae, that create a wound to facilitate toxin delivery. Some protists discharge harpoon-like extrusomes (toxicysts and nematocysts) that penetrate their prey and deliver toxins. Many bacteria possess secretion systems or contractile injection systems that can introduce toxins into targets via wounds. Viruses, though not "true" organisms according to many, include a group (the bacteriophages) which can inject nucleic acids and virion proteins into host cells that inflict damage rivaling that of conventional venoms. Collectively, these examples suggest that venom delivery systems-and even toxungen delivery systems, which we briefly address-are much more widespread than previously recognized. Thus, our understanding of venom as an evolutionary novelty has focused on only a small proportion of venomous organisms. With regard to this widespread form of toxin deployment, the words of the Sherman Brothers in Disney's iconic tune, It's a Small World, could hardly be more apt: "There's so much that we share, that it's time we're aware, it's a small world after all".

Quality assessment strategy development and analytical method selection of GMP grade biological drugs for gene and cell therapy

Biological drugs with gene and cell therapy potentials, including natural or rationally created biomacromolecules, recombinant proteins/enzymes, gene-carrying DNA/RNA fragments, oncolytic viruses, plasmid and viral vectors or other gene delivering vehicles with specific therapeutic genes and gene manipulation tools, and genetically modified and reprogrammed human cells comprise a large fraction of drug development candidates in modern precision and regeneration medicine. These drugs have displayed unique capabilities in treating patients with previously incurable diseases. However, most of the drug preparations have complex multimolecular structures and require specific biomanufacturing systems and many other additional biological active materials for drug synthesis, cell expansion, and production enhancement. Thus, the final products would have to be subjected to sequential extensive purification processes to exclude impurities and to concentrate the drug products after manufacturing. The quality evaluation for each drug product is an individualized process and must be specifically designed and performed according to the characteristics of the drug and its manufacturing and purification methods. Some of the Quality Control (QC) assays may be very costly and time-consuming, frequently with inconsistent test results from batch-to-batch. This review focuses on QC assessment strategy development for common gene and cell therapy drugs which use prokaryotic or eukaryotic cells for manufacturing or cell factories for in vitro expansions, especially for drug identification and concentration determination, impurity detection and quantification, drug potency, stability, and safety evaluations; and discusses some key issues for drug quality assessments in different categories and emphasizes the importance of individualized QC strategy design.

Receptor clustering tunes and sharpens the selectivity of multivalent binding

The immune system exploits a wide range of strategies to combine sensitivity with selectivity for optimal response. We propose a generic physical mechanism that allows tuning the location and steepness of the response threshold of cellular processes activated by multivalent binding. The mechanism is based on the possibility to modulate the attraction between membrane receptors. We use theory and simulations to show how tuning interreceptor attraction can enhance or suppress the binding of multivalent ligand-coated particles to surfaces. The changes in the interreceptor attraction less than the thermal energy kBT can selectively switch the receptor-clustering and activation on or off in an almost step-wise fashion, which we explain by near-critical receptor density fluctuations. We also show that the same mechanism can efficiently regulate the onset of endocytosis for, e.g., drug delivery vehicles.

Human Riboviruses: A Comprehensive Study

The urgency to understand the complex interactions between viruses, their animal reservoirs, and human populations has been necessitated by the continuous spread of zoonotic viral diseases as evidenced in epidemics and pandemics throughout human history. Riboviruses are involved in some of the most prevalent human diseases, responsible for causing epidemics and pandemics. These viruses have an animal origin and have been known to cross the inter-species barrier time and time again, eventually infecting human beings. Their evolution has been a long road to harbour important adaptations for increasing fitness, mutability and virulence; a result of natural selection and mutation pressure, making these viruses highly infectious and difficult to counter. Accumulating favourable mutations in the course, they imitate the GC content and codon usage patterns of the host for maximising the chances of infection. A myriad of viral and host factors determine the fate of specific viral infections, which may include virus protein and host receptor compatibility, host restriction factors and others. Thus, understanding the biology, transmission and molecular mechanisms of Riboviruses is essential for the development of effective antiviral treatments, vaccine development and strategies to prevent and control viral infections. Keeping these aspects in mind, this review aims to provide a holistic approach towards understanding Riboviruses.

Dipeptidyl peptidase 4 is a cofactor for porcine epidemic diarrhea virus infection

Porcine epidemic diarrhea virus (PEDV) is a member of the genus Alphacoronavirus in the family Coronaviridae, which has a mortality rate of up to 100 % in neonatal piglets and causes huge economic losses to the pig industry. The target cells of PEDV infection are porcine small intestinal epithelial cells, and the mechanism of PEDV invasion remains unclear. Our study found that dipeptidyl peptidase 4 (DPP4) acts as a cofactor for PEDV infection by promoting PEDV invasion and replication. Firstly, we mapped the expression profile of DPP4 in different tissues of 7-day-old piglets and found that DPP4 was highly expressed in the liver, lung, kidney, duodenum, jejunum, and ileum tissues of piglets. In addition, the immunohistochemical results showed that DPP4 was mainly distributed at the apical of intestinal villous epithelial cells in the jejunum of piglets. Further studies revealed that DPP4 expression was significantly lower in PEDV-infected porcine jejunal tissues and IPEC-J2 cells than in uninfected controls. PEDV invasion and replication could be inhibited by DPP4 inhibitor and specific antibody. Moreover, DPP4 knockout was able to significantly inhibit PEDV infection. Then, we found that endogenous DPP4 interacted with PEDV, and that preincubation of PEDV with endogenous DPP4 reduced viral infection. Finally, we predicted the docking of DPP4 and PEDV-S1-RBD proteins in silico, showing a strong binding tendency. Taken together, our study supports the hypothesis that DPP4 is a cofactor for PEDV infection.

(R)evolution of Viruses: Introduction to biothermodynamics of viruses

As of 26 April 2024, the International Committee on Taxonomy of Viruses has registered 14690 virus species. Of these, only several dozen have been chemically and thermodynamically characterized. Every virus species is characterized by a specific empirical formula and thermodynamic properties - enthalpy, entropy and Gibbs energy. These physical properties are used in a mechanistic model of virus-host interactions at the cell membrane and in the cytoplasm. This review article presents empirical formulas and Gibbs energies for all major variants of SARS-CoV-2. This article also reports and suggests a mechanistic model of evolutionary changes, with the example of time evolution of SARS-CoV-2 from 2019 to 2024.

Viral entry mechanisms: the role of molecular simulation in unlocking a key step in viral infections

Viral infections are a major global health concern, affecting millions of people each year. Viral entry is one of the crucial stages in the infection process, but its details remain elusive. Enveloped viruses are enclosed by a lipid membrane that protects their genetic material and these viruses are linked to various human illnesses, including influenza, and COVID-19. Due to the advancements made in the field of molecular simulation, significant progress has been made in unraveling the dynamic processes involved in viral entry of enveloped viruses. Simulation studies have provided deep insight into the function of the proteins responsible for attaching to the host receptors and promoting membrane fusion (fusion proteins), deciphering interactions between these proteins and receptors, and shedding light on the functional significance of key regions, such as the fusion peptide. These studies have already significantly contributed to our understanding of this critical aspect of viral infection and assisted the development of effective strategies to combat viral diseases and improve global health. This review focuses on the vital role of fusion proteins in facilitating the entry process of enveloped viruses and highlights the contributions of molecular simulation studies to uncover the molecular details underlying their mechanisms of action.

Painting Cell-Cell Interactions by Horseradish Peroxidase and Endogenously Generated Hydrogen Peroxide

Cell-cell interactions are fundamental in biology for maintaining physiological conditions with direct contact being the most straightforward mode of interaction. Recent advancements have led to the development of various chemical tools for detecting or identifying these interactions. However, the use of exogenous cues, such as toxic reagents, bulky probes, and light irradiation, can disrupt normal cell physiology. For example, the toxicity of hydrogen peroxide (H2O2) limits the applications of peroxidases in the proximity labeling field. In this study, we aimed to address this limitation by demonstrating that membrane-localized horseradish peroxidase (HRP-TM) efficiently utilizes endogenously generated extracellular H2O2. By harnessing endogenous H2O2, we observed that HRP-TM-expressing cells can effectively label contacting cells without the need for exogenous H2O2 treatment. Furthermore, we confirmed that HRP-TM labels proximal cells in an interaction-dependent manner. These findings offer a novel approach for studying cell-cell interactions under more physiological conditions without the confounding effects of exogenous stimuli. Our study contributes to elucidating cell-cell interaction networks in various model organisms, providing valuable insights into the dynamic interplay between cells in their native network.

Cyclic peptides: A powerful instrument for advancing biomedical nanotechnologies and drug development

Cyclic peptides have emerged as an essential tool in the advancement of biomedical nanotechnologies, offering unique structural and functional advantages over linear peptides. This review article aims to highlight the roles of cyclic peptides in the development of biomedical fields, with a particular focus on their application in drug discovery and delivery. Cyclic peptides exhibit exceptional stability, bioavailability, and binding specificity, making them ideal candidates for therapeutic and diagnostic applications. We explore the synthesis and design strategies that enable the precise control of cyclic peptide structures, leading to enhanced performance in targeting specific cellular pathways. The article also highlights recent breakthroughs in the use of cyclic peptides for creating innovative drug delivery systems, including nanoparticle conjugates and peptide-drug conjugates, which have shown promise in improving the efficacy and safety profiles of existing traditional treatments. The integration of cyclic peptides into nanotechnological frameworks holds significant promise for addressing unmet medical needs, providing a foundation for future advancements in personalized medicine and targeted drug delivery.

Role of surface glycans in enveloped RNA virus infections: A structural perspective

Enveloped RNA viruses have been causative agents of major pandemic outbreaks in the recent past. Glycans present on these virus surface proteins are critical for multiple processes during the viral infection cycle. Presence of glycans serves as a key determinant of immunogenicity, but intrinsic heterogeneity, dynamics, and evolutionary shifting of glycans in heavily glycosylated enveloped viruses confounds typical structure-function analysis. Glycosylation sites are also conserved across different viral families, which further emphasizes their functional significance. In this review, we summarize findings regarding structure-function correlation of glycans on enveloped RNA virus proteins.

Exploring the influence of anionic lipids in the host cell membrane on viral fusion

Membrane fusion is an essential component of the viral lifecycle that allows the delivery of the genetic information of the virus into the host cell. Specialized viral glycoproteins exist on the surface of mature virions where they facilitate fusion through significant conformational changes, ultimately bringing opposing membranes into proximity until they eventually coalesce. This process can be positively influenced by a number of specific cellular factors such as pH, enzymatic cleavage, divalent ions, and the composition of the host cell membrane. In this review, we have summarized how anionic lipids have come to be involved in viral fusion and how the endosomal resident anionic lipid BMP has become increasingly implicated as an important cofactor for those viruses that fuse via the endocytic pathway.

Antiviral Potential and In Silico Insights of Polyphenols as Sustainable Phytopharmaceuticals: A Comprehensive Review

Polyphenols, particularly flavonoids, are reported to have health-promoting, disease-preventing abilities and several polyphenols having a wide spectrum of antiviral activities can be explored for preventive and/or therapeutic purposes. We have compiled the updated literature of diverse polyphenols active against common viral diseases, including herpes, hepatitis, influenza, rota and SARS-corona-viruses. The antiviral activity of bioactive polyphenols depends on the hydroxyl and ester groups of polyphenol molecules, as compounds with five or more hydroxyl groups and three specific methoxy groups showed antiviral potential, like anti-rabies activity. This comprehensive review will explore selective polyphenols isolated from common ethnomedicinal or food plants. Comparing bioactivities of structurally related polyphenols and using bioinformatics studies, we have explored the three most promising phyto-antivirals, including chrysin, resveratrol and quercetin, available in many foods and medicinal plants. Quercetin showed a maximum interaction score with human genes. We also explore the intricate structure-activity relationship between these polyphenols and pathogenic viruses with their mechanisms of antiviral action in selected virus models. Here, we report the promising potential of some phyto-polyphenols in the management of viral diseases through an in-depth analysis of the structure and bioactivity of these compounds.

Identification and Targeting of Regulators of SARS-CoV-2-Host Interactions in the Airway Epithelium

Although the impact of SARS-CoV-2 in the lung has been extensively studied, the molecular regulators and targets of the host-cell programs hijacked by the virus in distinct human airway epithelial cell populations remain poorly understood. This is in part ascribed to the use of nonprimary cell systems, overreliance on single-cell gene expression profiling that does not ultimately reflect protein activity, and bias toward the downstream effects rather than their mechanistic determinants. Here we address these issues by network-based analysis of single cell transcriptomic profiles of pathophysiologically relevant human adult basal, ciliated and secretory cells to identify master regulator (MR) protein modules controlling their SARS-CoV-2-mediated reprogramming. This uncovered chromatin remodeling, endosomal sorting, ubiquitin pathways, as well as proviral factors identified by CRISPR analyses as components of the host response collectively or selectively activated in these cells. Large-scale perturbation assays, using a clinically relevant drug library, identified 11 drugs able to invert the entire MR signature activated by SARS-CoV-2 in these cell types. Leveraging MR analysis and perturbational profiles of human primary cells represents a novel mechanism-based approach and resource that can be directly generalized to interrogate signatures of other airway conditions for drug prioritization.

Bioinformatic Resources for Exploring Human-virus Protein-protein Interactions Based on Binding Modes

Historically, there have been many outbreaks of viral diseases that have continued to claim millions of lives. Research on human-virus protein-protein interactions (PPIs) is vital to understanding the principles of human-virus relationships, providing an essential foundation for developing virus control strategies to combat diseases. The rapidly accumulating data on human-virus PPIs offer unprecedented opportunities for bioinformatics research around human-virus PPIs. However, available detailed analyses and summaries to help use these resources systematically and efficiently are lacking. Here, we comprehensively review the bioinformatic resources used in human-virus PPI research, and discuss and compare their functions, performance, and limitations. This review aims to provide researchers with a bioinformatic toolbox that will hopefully better facilitate the exploration of human-virus PPIs based on binding modes.

Pathogenicity and virulence of chikungunya virus

Chikungunya virus (CHIKV) is a mosquito-transmitted, RNA virus that causes an often-severe musculoskeletal illness characterized by fever, joint pain, and a range of debilitating symptoms. The virus has re-emerged as a global health threat in recent decades, spreading from its origin in Africa across Asia and the Americas, leading to widespread outbreaks impacting millions of people. Despite more than 50 years of research into the pathogenesis of CHIKV, there is still no curative treatment available. Current management of CHIKV infections primarily involves providing supportive care to alleviate symptoms and improve the patient's quality of life. Given the ongoing threat of CHIKV, there is an urgent need to better understand its pathogenesis. This understanding is crucial for deciphering the mechanisms underlying the disease and for developing effective strategies for both prevention and management. This review aims to provide a comprehensive overview of CHIKV and its pathogenesis, shedding light on the complex interactions of viral genetics, host factors, immune responses, and vector-related factors. By exploring these intricate connections, the review seeks to contribute to the knowledge base surrounding CHIKV, offering insights that may ultimately lead to more effective prevention and management strategies for this re-emerging global health threat.

Characterization and Fluctuations of an Ivermectin Binding Site at the Lipid Raft Interface of the N-Terminal Domain (NTD) of the Spike Protein of SARS-CoV-2 Variants

Most studies on the docking of ivermectin on the spike protein of SARS-CoV-2 concern the receptor binding domain (RBD) and, more precisely, the RBD interface recognized by the ACE2 receptor. The N-terminal domain (NTD), which controls the initial attachment of the virus to lipid raft gangliosides, has not received the attention it deserves. In this study, we combined molecular modeling and physicochemical approaches to analyze the mode of interaction of ivermectin with the interface of the NTD-facing lipid rafts of the host cell membrane. We characterize a binding area that presents point mutations and deletions in successive SARS-CoV-2 variants from the initial strain to omicron KP.3 circulating in many countries in 2024. We show that ivermectin has exceptional flexibility, allowing the drug to bind to the spike protein of all variants tested. The energy of interaction is specific to each variant, allowing a classification according to their affinity for ivermectin in the following ascending order: Omicron KP.3 < Delta < Omicron BA.5 < Alpha < Wuhan (B.1) < Omicron BA.1. The binding site of ivermectin is subject to important variations of the NTD, including the Y144 deletion. It overlaps with the ganglioside binding domain of the NTD, as demonstrated by docking and physicochemical studies. These results suggest a new mechanism of antiviral action for ivermectin based on competitive inhibition for initial virus attachment to lipid rafts. The current KP.3 variant is still recognized by ivermectin, although with an affinity slightly lower than the Wuhan strain.

Rapid Development of Small Rodent Animal Models for Infectious Disease Research Through Vectorized Receptor Molecule Expression

The emergence and re-emergence of pathogens with pandemic potential has been a persistent issue throughout history. Recent decades have seen significant outbreaks of zoonotic viruses from members of the Coronaviridae, Filoviridae, Paramyxoviridae, Flaviviridae, and Togaviridae families, resulting in widespread infections. The continual emergence of zoonotic viral pathogens and associated infections highlights the need for prevention strategies and effective treatments. Central to this effort is the availability of suitable animal models, which are essential for understanding pathogenesis and assessing transmission dynamics. These animals are also critical for evaluating the safety and efficacy of novel vaccines or therapeutics and are essential in facilitating regulatory approval of new products. Rapid development of animal models is an integral aspect of pandemic response and preparedness; however, their establishment is fraught by several rate-limiting steps, including selection of a suitable species, the logistical challenges associated with sharing and disseminating transgenic animals (e.g., the time-intensive nature of breeding and maintaining colonies), the availability of technical expertise, as well as ethical and regulatory approvals. A method for the rapid development of relevant animal models that has recently gained traction, in large part due to the COVID-19 pandemic, is the use of gene therapy vectors to express human viral receptors in readily accessible laboratory animals to enable virus infection and development of clinical disease. These models can be developed rapidly on any genetic background, making mechanistic studies and accelerated evaluation of novel countermeasures possible. In this review, we will discuss important considerations for the effective development of animal models using viral vector approaches and review the current vector-based animal models for studying viral pathogenesis and evaluating prophylactic and therapeutic strategies, with an emphasis on models of SARS-CoV-2 infection based on the vectorized expression of human angiotensin-converting enzyme 2.

Enterovirus Antibodies: Friends and Foes

Enteroviruses (EV) initiate replication by binding to their cellular receptors, leading to the uncoating and release of the viral genome into the cytosol of the host cell. Neutralising antibodies (NAbs) binding to epitopes on enteroviral capsid proteins can inhibit this infectious process through several mechanisms of neutralisation in vitro. Fc-mediated antibody effector functions such as antibody-dependent cell-mediated cytotoxicity and antibody-dependent cellular phagocytosis have also been described for some EV. However, antibody binding to virions does not always result in viral neutralisation. Non-neutralising antibodies, or sub-neutralising concentrations of antibodies, can enhance infection of viruses, leading to more severe pathologies. This phenomenon, known as antibody-dependent enhancement (ADE) of infection, has been described in vitro and/or in vivo for EV including poliovirus, coxsackievirus B and EV-A71. It has been shown that ADE of EV infection is mediated by FcγRs expressed by monocytes, macrophages, B lymphocytes and granulocytes. Antibodies play a crucial role in the diagnosis and monitoring of infections. They are valuable markers that have been used to establish a link between enteroviral infection and chronic diseases such as type 1 diabetes. Monoclonal and polyclonal antibodies targeting enteroviral proteins have been developed and shown to be effective to prevent or combat EV infections in vitro and in vivo. In addition, vaccines are under development, and clinical trials of vaccines are underway or have been completed, providing hope for the prevention of diseases due to EV. However, the ADE of the infection should be considered in the development of anti-EV antibodies or safe vaccines.

Computational design of prefusion-stabilized Herpesvirus gB trimers

In the absence of effective vaccines, human-infecting members of the Herpesvirus family cause considerable morbidity and mortality worldwide. Herpesvirus infection relies on receptor engagement by a gH/gL glycoprotein complex which induces large-scale conformational changes of the gB glycoprotein to mediate fusion of the viral and host membranes and infection. The instability of all herpesvirus gBs have hindered biochemical and functional studies, thereby limiting our understanding of the infection mechanisms of these pathogens and preventing vaccine design. Here, we computationally stabilized and structurally characterized the Epstein-Barr virus prefusion gB ectodomain trimer, providing an atomic-level description of this key therapeutic target. We show that this stabilization strategy is broadly applicable to other herpesvirus gB trimers and identified conformational intermediates supporting a previously unanticipated mechanism of gB-mediated fusion. These findings provide a blueprint to develop vaccine candidates for these pathogens with major public health burden.

Quantification of the interaction forces between dengue virus and dopamine type-2 receptor using optical tweezers

BACKGROUND

Dengue virus (DENV) causes the most significant mosquito-borne viral disease with a wide spectrum of clinical manifestation, including neurological symptoms associated with lethal dengue diseases. Dopamine receptors are expressed in central nervous system, and dopamine antagonists have been reported to exhibit antiviral activity against DENV infection in vivo and in vitro. Although identification of host-cell receptor is critical to understand dengue neuropathogenesis and neurotropism, the involvement of dopamine receptors in DENV infection remains unclear.

RESULTS

We exploited the sensitivity and precision of force spectroscopy to address whether dopamine type-2 receptors (D2R) directly interact with DENV particles at the first step of infection. Using optical tweezers, we quantified and characterized DENV binding to D2R expressed on Chinese hamster ovary (CHO) cells. Our finding suggested that the binding was D2R- and DENV-dependent, and that the binding force was in the range of 50-60 pN. We showed that dopamine antagonists prochlorperazine (PCZ) and trifluoperazine (TFP), previously reported to inhibit dengue infection, interrupt the DENV-D2R specific binding.

CONCLUSIONS

This study demonstrates that D2R could specifically recognize DENV particles and function as an attachment factor on cell surfaces for DENV. We propose D2R as a host receptor for DENV and as a potential therapeutic target for anti-DENV drugs.

Elucidating the inhibitory mechanism of Zika virus NS2B-NS3 protease with dipeptide inhibitors: Insights from molecular docking and molecular dynamics simulations

Microcephaly, Guillain-Barré syndrome, and potential sexual transmission stand as prominent complications associated with Zika virus (ZIKV) infection. The absence of FDA-approved drugs or vaccines presents a substantial obstacle in combatting the virus. Furthermore, the inclusion of pregnancy in the pharmacological screening process complicates and extends the endeavor to ensure molecular safety and minimal toxicity. Given its pivotal role in viral assembly and maturation, the NS2B-NS3 viral protease emerges as a promising therapeutic target against ZIKV. In this context, a dipeptide inhibitor was specifically chosen as a control against 200 compounds for docking analysis. Subsequent molecular dynamics simulations extending over 200 ns were conducted to ascertain the stability of the docked complex and confirm the binding of the inhibitor at the protein's active site. The simulation outcomes exhibited conformity to acceptable thresholds, encompassing parameters such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), ligand-protein interaction analysis, ligand characterization, and surface area analysis. Notably, analysis of ligand angles bolstered the identification of prospective ligands capable of inhibiting viral protein activity and impeding virus dissemination. In this study, the integration of molecular docking and dynamics simulations has pinpointed the dipeptide inhibitor as a potential candidate ligand against ZIKV protease, thereby offering promise for therapeutic intervention against the virus.

Potential Effects of Hyperglycemia on SARS-CoV-2 Entry Mechanisms in Pancreatic Beta Cells

The COVID-19 pandemic has revealed a bidirectional relationship between SARS-CoV-2 infection and diabetes mellitus. Existing evidence strongly suggests hyperglycemia as an independent risk factor for severe COVID-19, resulting in increased morbidity and mortality. Conversely, recent studies have reported new-onset diabetes following SARS-CoV-2 infection, hinting at a potential direct viral attack on pancreatic beta cells. In this review, we explore how hyperglycemia, a hallmark of diabetes, might influence SARS-CoV-2 entry and accessory proteins in pancreatic β-cells. We examine how the virus may enter and manipulate such cells, focusing on the role of the spike protein and its interaction with host receptors. Additionally, we analyze potential effects on endosomal processing and accessory proteins involved in viral infection. Our analysis suggests a complex interplay between hyperglycemia and SARS-CoV-2 in pancreatic β-cells. Understanding these mechanisms may help unlock urgent therapeutic strategies to mitigate the detrimental effects of COVID-19 in diabetic patients and unveil if the virus itself can trigger diabetes onset.

Significance of Artificial Intelligence in the Study of Virus-Host Cell Interactions

A highly critical event in a virus's life cycle is successfully entering a given host. This process begins when a viral glycoprotein interacts with a target cell receptor, which provides the molecular basis for target virus-host cell interactions for novel drug discovery. Over the years, extensive research has been carried out in the field of virus-host cell interaction, generating a massive number of genetic and molecular data sources. These datasets are an asset for predicting virus-host interactions at the molecular level using machine learning (ML), a subset of artificial intelligence (AI). In this direction, ML tools are now being applied to recognize patterns in these massive datasets to predict critical interactions between virus and host cells at the protein-protein and protein-sugar levels, as well as to perform transcriptional and translational analysis. On the other end, deep learning (DL) algorithms-a subfield of ML-can extract high-level features from very large datasets to recognize the hidden patterns within genomic sequences and images to develop models for rapid drug discovery predictions that address pathogenic viruses displaying heightened affinity for receptor docking and enhanced cell entry. ML and DL are pivotal forces, driving innovation with their ability to perform analysis of enormous datasets in a highly efficient, cost-effective, accurate, and high-throughput manner. This review focuses on the complexity of virus-host cell interactions at the molecular level in light of the current advances of ML and AI in viral pathogenesis to improve new treatments and prevention strategies.

Sialic Acid Receptor Specificity in Mammary Gland of Dairy Cattle Infected with Highly Pathogenic Avian Influenza A(H5N1) Virus

In March 2024, the US Department of Agriculture's Animal and Plant Health Inspection Service reported detection of highly pathogenic avian influenza (HPAI) A(H5N1) virus in dairy cattle in the United States for the first time. One factor that determines susceptibility to HPAI H5N1 infection is the presence of specific virus receptors on host cells; however, little is known about the distribution of the sialic acid (SA) receptors in dairy cattle, particularly in mammary glands. We compared the distribution of SA receptors in the respiratory tract and mammary gland of dairy cattle naturally infected with HPAI H5N1. The respiratory and mammary glands of HPAI H5N1-infected dairy cattle are rich in SA, particularly avian influenza virus-specific SA α2,3-gal. Mammary gland tissues co-stained with sialic acids and influenza A virus nucleoprotein showed predominant co-localization with the virus and SA α2,3-gal. HPAI H5N1 exhibited epitheliotropism within the mammary gland, and we observed rare immunolabeling within macrophages.

Neurological manifestations of Flaviviridae, Togaviridae, and Peribunyaviridae as vector-borne viruses

Vector-borne viruses pose a significant health problem worldwide, as they are transmitted to humans through the bite of infected arthropods such as mosquitoes and ticks. In recent years, emerging and re-emerging vector-borne diseases have gained attention as they can cause a wide spectrum of neurological manifestations. The neurological manifestations of vector-borne viruses encompass a board spectrum of clinical manifestations, ranging from mild and self-limiting symptoms to severe and life-threatening conditions. Common neurological complications include viral encephalitis, acute flaccid paralysis, aseptic meningitis, and various neuromuscular disorders. The specific viruses responsible for these neurological sequelae vary by geographic region and include Orthoflavivirus nilense, Zika virus, dengue virus, chikungunya virus, Japanese encephalitis virus, and tick-borne encephalitis virus. This review focuses on the pathogenesis of these neurologic complications and highlights the mechanisms by which vector-borne viruses invade the central nervous system and trigger neuroinflammatory responses. Diagnostic challenges and strategies for early detection of neurological manifestations are discussed, emphasising the importance of clinical suspicion and advanced laboratory testing.

TurboID-mediated proximity labeling technologies to identify virus co-receptors

Virus receptors determine the tissue tropism of viruses and have a certain relationship with the clinical outcomes caused by viral infection, which is of great importance for the identification of virus receptors to understand the infection mechanism of viruses and to develop entry inhibitor. Proximity labeling (PL) is a new technique for studying protein-protein interactions, but it has not yet been applied to the identification of virus receptors or co-receptors. Here, we attempt to identify co-receptor of SARS-CoV-2 by employing TurboID-catalyzed PL. The membrane protein angiotensin-converting enzyme 2 (ACE2) was employed as a bait and conjugated to TurboID, and a A549 cell line with stable expression of ACE2-TurboID was constructed. SARS-CoV-2 pseudovirus were incubated with ACE2-TurboID stably expressed cell lines in the presence of biotin and ATP, which could initiate the catalytic activity of TurboID and tag adjacent endogenous proteins with biotin. Subsequently, the biotinylated proteins were harvested and identified by mass spectrometry. We identified a membrane protein, AXL, that has been functionally shown to mediate SARS-CoV-2 entry into host cells. Our data suggest that PL could be used to identify co-receptors for virus entry.

microRNA-guided immunity against respiratory virus infection in human and mouse lung cells

Viral infectivity depends on multiple factors. Recent studies showed that the interaction between viral RNAs and endogenous microRNAs (miRNAs) regulates viral infectivity; viral RNAs function as a sponge of endogenous miRNAs and result in upregulation of its original target genes, while endogenous miRNAs target viral RNAs directly and result in repression of viral gene expression. In this study, we analyzed the possible interaction between parainfluenza virus RNA and endogenous miRNAs in human and mouse lungs. We showed that the parainfluenza virus can form base pairs with human miRNAs abundantly than mouse miRNAs. Furthermore, we analyzed that the sponge effect of endogenous miRNAs on viral RNAs may induce the upregulation of transcription regulatory factors. Then, we performed RNA-sequence analysis and observed the upregulation of transcription regulatory factors in the early stages of parainfluenza virus infection. Our studies showed how the differential expression of endogenous miRNAs in lungs could contribute to respiratory virus infection and species- or tissue-specific mechanisms and common mechanisms could be conserved in humans and mice and regulated by miRNAs during viral infection.

Antibody nanoparticle conjugate-based targeted immunotherapy for non-small cell lung cancer

The use of immune checkpoint inhibitors, which activate T cells, is a paradigm shift in the treatment of non-small cell lung cancer. However, the overall response remains low. To address this limitation, here we describe a novel platform, termed antibody-conjugated drug-loaded nanotherapeutics (ADN), which combines immunotherapy and molecularly targeted therapy. An ADN was designed with an anti-CD47 and anti-programmed death ligand 1 (PDL1) antibody pair on the surface of the nanoparticle and a molecularly targeted inhibitor of the PI3K (phosphatidylinositol 3-kinase)/AKT/mTOR (mammalian target of rapamycin) pathway, PI103, entrapped in the nanoparticle. The anti-CD47-PDL1-ADN exhibited greater antitumor efficacy than current treatment options with a PDL1 inhibitor in vivo in an aggressive lung cancer immunocompetent mouse model. Dual antibody-drug-loaded nanotherapeutics can emerge as an attractive platform to improve outcomes with cancer immunotherapy.

NRP1 is a receptor for mammalian orthoreovirus engaged by distinct capsid subunits

Mammalian orthoreovirus (reovirus) is a nonenveloped virus that establishes primary infection in the intestine and disseminates to sites of secondary infection, including the CNS. Reovirus entry involves multiple engagement factors, but how the virus disseminates systemically and targets neurons remains unclear. In this study, we identified murine neuropilin 1 (mNRP1) as a receptor for reovirus. mNRP1 binds reovirus with nanomolar affinity using a unique mechanism of virus-receptor interaction, which is coordinated by multiple interactions between distinct reovirus capsid subunits and multiple NRP1 extracellular domains. By exchanging essential capsid protein-encoding gene segments, we determined that the multivalent interaction is mediated by outer-capsid protein σ3 and capsid turret protein λ2. Using capsid mutants incapable of binding NRP1, we found that NRP1 contributes to reovirus dissemination and neurovirulence in mice. Collectively, our results demonstrate that NRP1 is an entry receptor for reovirus and uncover mechanisms by which NRPs promote viral entry and pathogenesis.

Intrinsic Disorder in the Host Proteins Entrapped in Rabies Virus Particles

A proteomics analysis of purified rabies virus (RABV) revealed 47 entrapped host proteins within the viral particles. Out of these, 11 proteins were highly disordered. Our study was particularly focused on five of the RABV-entrapped mouse proteins with the highest levels of disorder: Neuromodulin, Chmp4b, DnaJB6, Vps37B, and Wasl. We extensively utilized bioinformatics tools, such as FuzDrop, D2P2, UniProt, RIDAO, STRING, AlphaFold, and ELM, for a comprehensive analysis of the intrinsic disorder propensity of these proteins. Our analysis suggested that these disordered host proteins might play a significant role in facilitating the rabies virus pathogenicity, immune system evasion, and the development of antiviral drug resistance. Our study highlighted the complex interaction of the virus with its host, with a focus on how the intrinsic disorder can play a crucial role in virus pathogenic processes, and suggested that these intrinsically disordered proteins (IDPs) and disorder-related host interactions can also be a potential target for therapeutic strategies.

Conversion of Host Cell Receptor into Virus Destructor by Immunodisc to Neutralize Diverse SARS-CoV-2 Variants

The decreasing efficacy of antiviral drugs due to viral mutations highlights the challenge of developing a single agent targeting multiple strains. Using host cell viral receptors as competitive inhibitors is promising, but their low potency and membrane-bound nature have limited this strategy. In this study, the authors show that angiotensin-converting enzyme 2 (ACE2) in a planar membrane patch can effectively neutralize all tested severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that emerged during the COVID-19 pandemic. The ACE2-incorporated membrane patch implemented using nanodiscs replicated the spike-mediated membrane fusion process outside the host cell, resulting in virus lysis, extracellular RNA release, and potent antiviral activity. While neutralizing antibodies became ineffective as the SARS-CoV-2 evolved to better penetrate host cells the ACE2-incorporated nanodiscs became more potent, highlighting the advantages of using receptor-incorporated nanodiscs for antiviral purposes. ACE2-incorporated immunodisc, an Fc fusion nanodisc developed in this study, completely protected humanized mice infected with SARS-CoV-2 after prolonged retention in the airways. This study demonstrates that the incorporation of viral receptors into immunodisc transforms the entry gate into a potent virucide for all current and future variants, a concept that can be extended to different viruses.

Upregulation of mRNA Expression of ADGRD1/GPR133 and ADGRG7/GPR128 in SARS-CoV-2-Infected Lung Adenocarcinoma Calu-3 Cells

Adhesion G protein-coupled receptors (aGPCRs) play an important role in neurodevelopment, immune defence and cancer; however, their role throughout viral infections is mostly unexplored. We have been searching for specific aGPCRs involved in SARS-CoV-2 infection of mammalian cells. In the present study, we infected human epithelial cell lines derived from lung adenocarcinoma (Calu-3) and colorectal carcinoma (Caco-2) with SARS-CoV-2 in order to analyse changes in the level of mRNA encoding individual aGPCRs at 6 and 12 h post infection. Based on significantly altered mRNA levels, we identified four aGPCR candidates-ADGRB3/BAI3, ADGRD1/GPR133, ADGRG7/GPR128 and ADGRV1/GPR98. Of these receptors, ADGRD1/GPR133 and ADGRG7/GPR128 showed the largest increase in mRNA levels in SARS-CoV-2-infected Calu-3 cells, whereas no increase was observed with heat-inactivated SARS-CoV-2 and virus-cleared conditioned media. Next, using specific siRNA, we downregulated the aGPCR candidates and analysed SARS-CoV-2 entry, replication and infectivity in both cell lines. We observed a significant decrease in the amount of SARS-CoV-2 newly released into the culture media by cells with downregulated ADGRD1/GPR133 and ADGRG7/GPR128. In addition, using a plaque assay, we observed a reduction in SARS-CoV-2 infectivity in Calu-3 cells. In summary, our data suggest that selected aGPCRs might play a role during SARS-CoV-2 infection of mammalian cells.

Genomic Evolution and Recombination Dynamics of Human Adenovirus D Species: Insights from Comprehensive Bioinformatic Analysis

Human adenoviruses (HAdVs) can infect various epithelial mucosal cells, ultimately causing different symptoms in infected organ systems. With more than 110 types classified into seven species (A-G), HAdV-D species possess the highest number of viruses and are the fastest proliferating. The emergence of new adenovirus types and increased diversity are driven by homologous recombination (HR) between viral genes, primarily in structural elements such as the penton base, hexon and fiber proteins, and the E1 and E3 regions. A comprehensive analysis of the HAdV genome provides valuable insights into the evolution of human adenoviruses and identifies genes that display high variation across the entire genome to determine recombination patterns. Hypervariable regions within genetic sequences correlate with functional characteristics, thus allowing for adaptation to new environments and hosts. Proteotyping of newly emerging and already established adenoviruses allows for prediction of the characteristics of novel viruses. HAdV-D species evolved in a direction that increased diversity through gene recombination. Bioinformatics analysis across the genome, particularly in highly variable regions, allows for the verification or re-evaluation of recombination patterns in both newly introduced and pre-existing viruses, ultimately aiding in tracing various biological traits such as virus tropism and pathogenesis. Our research does not only assist in predicting the emergence of new adenoviruses but also offers critical guidance in regard to identifying potential regulatory factors of homologous recombination hotspots.

Lytic/Lysogenic Transition as a Life-History Switch

The transition between lytic and lysogenic life cycles is the most important feature of the life-history of temperate viruses. To explain this transition, an optimal life-history model is offered based a discrete-time formulation of phage/bacteria population dynamics that features infection of bacteria by Poisson sampling of virions from the environment. The time step is the viral latency period. In this model, density-dependent viral absorption onto the bacterial surface produces virus/bacteria coexistence and density dependence in bacterial growth is not needed. The formula for the transition between lytic and lysogenic phases is termed the 'fitness switch'. According to the model, the virus switches from lytic to lysogenic when its population grows faster as prophage than as virions produced by lysis of the infected cells, and conversely for the switch from lysogenic to lytic. A prophage that benefits the bacterium it infects automatically incurs lower fitness upon exiting the bacterial genome, resulting in its becoming locked into the bacterial genome in what is termed here as a 'prophage lock'. The fitness switch qualitatively predicts the ecogeographic rule that environmental enrichment leads to microbialization with a concomitant increase in lysogeny, fluctuating environmental conditions promote virus-mediated horizontal gene transfer, and prophage-containing bacteria can integrate into the microbiome of a eukaryotic host forming a functionally integrated tripartite holobiont. These predictions accord more with the 'Piggyback-the-Winner' hypothesis than with the 'Kill-the-Winner' hypothesis in virus ecology.

C1QTNF5 is a novel attachment factor that facilitates the entry of influenza A virus

Influenza A virus (IAV) binds sialic acid receptors on the cell surface to enter the host cells, which is the key step in initiating infection, transmission and pathogenesis. Understanding the factors that contribute to the highly efficient entry of IAV into human cells will help elucidate the mechanism of viral entry and pathogenicity, and provide new targets for intervention. In the present study, we reported a novel membrane protein, C1QTNF5, which binds to the hemagglutinin protein of IAV and promotes IAV infection in vitro and in vivo. We found that the HA1 region of IAV hemagglutinin is critical for the interaction with C1QTNF5 protein, and C1QTNF5 interacts with hemagglutinin mainly through its N-terminus (1-103 aa). In addition, we further demonstrated that overexpression of C1QTNF5 promotes IAV entry, while blocking the interaction between C1QTNF5 and IAV hemagglutinin greatly inhibits viral entry. However, C1QTNF5 does not function as a receptor to mediate IAV infection in sialic acid-deficient CHO-Lec2 cells, but promotes IAV to attach to these cells, suggesting that C1QTNF5 is an important attachment factor for IAV. This work reveals C1QTNF5 as a novel IAV attachment factor and provides a new perspective for antiviral strategies.

Vault RNAs (vtRNAs): Rediscovered non-coding RNAs with diverse physiological and pathological activities

The physicochemical characteristics of RNA admit non-coding RNAs to perform a different range of biological acts through various mechanisms and are involved in regulating a diversity of fundamental processes. Notably, some reports of pathological conditions have proved abnormal expression of many non-coding RNAs guides the ailment. Vault RNAs are a class of non-coding RNAs containing stem regions or loops with well-conserved sequence patterns that play a fundamental role in the function of vault particles through RNA-ligand, RNA-RNA, or RNA-protein interactions. Taken together, vault RNAs have been proposed to be involved in a variety of functions such as cell proliferation, nucleocytoplasmic transport, intracellular detoxification processes, multidrug resistance, apoptosis, and autophagy, and serve as microRNA precursors and signaling pathways. Despite decades of investigations devoted, the biological function of the vault particle or the vault RNAs is not yet completely cleared. In this review, the current scientific assertions of the vital vault RNAs functions were discussed.

Assessment of the broad-spectrum host targeting antiviral efficacy of halofuginone hydrobromide in human airway, intestinal and brain organotypic models

Halofuginone hydrobromide has shown potent antiviral efficacy against a variety of viruses such as SARS-CoV-2, dengue, or chikungunya virus, and has, therefore, been hypothesized to have broad-spectrum antiviral activity. In this paper, we tested this broad-spectrum antiviral activity of Halofuginone hydrobomide against viruses from different families (Picornaviridae, Herpesviridae, Orthomyxoviridae, Coronaviridae, and Flaviviridae). To this end, we used relevant human models of the airway and intestinal epithelium and regionalized neural organoids. Halofuginone hydrobomide showed antiviral activity against SARS-CoV-2 in the airway epithelium with no toxicity at equivalent concentrations used in human clinical trials but not against any of the other tested viruses.

Cellular receptors for mammalian viruses

The interaction of viral surface components with cellular receptors and other entry factors determines key features of viral infection such as host range, tropism and virulence. Despite intensive research, our understanding of these interactions remains limited. Here, we report a systematic analysis of published work on mammalian virus receptors and attachment factors. We build a dataset twice the size of those available to date and specify the role of each factor in virus entry. We identify cellular proteins that are preferentially used as virus receptors, which tend to be plasma membrane proteins with a high propensity to interact with other proteins. Using machine learning, we assign cell surface proteins a score that predicts their ability to function as virus receptors. Our results also reveal common patterns of receptor usage among viruses and suggest that enveloped viruses tend to use a broader repertoire of alternative receptors than non-enveloped viruses, a feature that might confer them with higher interspecies transmissibility.

Mannose-specific plant and microbial lectins as antiviral agents: A review

Lectins are non-immunological carbohydrate-binding proteins classified on the basis of their structure, origin, and sugar specificity. The binding specificity of such proteins with the surface glycan moiety determines their activity and clinical applications. Thus, lectins hold great potential as diagnostic and drug discovery agents and as novel biopharmaceutical products. In recent years, significant advancements have been made in understanding plant and microbial lectins as therapeutic agents against various viral diseases. Among them, mannose-specific lectins have being proven as promising antiviral agents against a variety of viruses, such as HIV, Influenza, Herpes, Ebola, Hepatitis, Severe Acute Respiratory Syndrome Coronavirus-1 (SARS-CoV-1), Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV) and most recent Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The binding of mannose-binding lectins (MBLs) from plants and microbes to high-mannose containing N-glycans (which may be simple or complex) of glycoproteins found on the surface of viruses has been found to be highly specific and mainly responsible for their antiviral activity. MBLs target various steps in the viral life cycle, including viral attachment, entry and replication. The present review discusses the brief classification and structure of lectins along with antiviral activity of various mannose-specific lectins from plants and microbial sources and their diagnostic and therapeutic applications against viral diseases.

Host range and cell recognition of archaeal viruses

Archaea are members of a separate domain of life that have unique properties, such as the composition of their cell walls and the structure of their lipid bilayers. Consequently, archaeal viruses face different challenges to infect host cells in comparison with viruses of bacteria and eukaryotes. Despite their significant impact on shaping microbial communities, our understanding of infection processes of archaeal viruses remains limited. Several receptors used by archaeal viruses to infect cells have recently been identified. The interactions between viruses and receptors are one of the determinants of the host range of viruses. Here, we review the current literature on host ranges of archaeal viruses and factors that might impact the width of these host ranges.

Proteome Analysis for Inflammation Related to Acute and Convalescent Infection

Infectious diseases are a significant burden in global healthcare. Pathogens engage with different host defense mechanisms. However, it is currently unknown if there are disease-specific immune signatures and/or if different pathogens elicit common immune-associated molecular entities to common therapeutic interventions. We studied patients enrolled through the Human Immunology Project Consortium (HIPC), which focuses on immune responses to various infections. Blood samples were collected and analyzed from patients during infection and follow-up time points at the convalescent stage. The study included samples from patients with Lyme disease (LD), tuberculosis (TB), malaria (MLA), dengue virus (DENV), and West Nile virus (WNV), as well as kidney transplant patients with cytomegalovirus (CMV) and polyomavirus (BKV) infections. Using an antibody-based assay, we quantified ~ 350 cell surface markers, cytokines, and chemokines involved in inflammation and immunity. Unique protein signatures were identified specific to the acute phase of infection irrespective of the pathogen type, with significant changes during convalescence. In addition, tumor necrosis factor receptor superfamily member 6 (TNR6), C-C Motif Chemokine Receptor 7 (CCR7), and C-C motif chemokine ligand-1 (CCL1) were increased in the acute and convalescent phases across all viral, bacterial, and protozoan compared to blood from healthy donors. Furthermore, despite the differences between pathogens, proteins were enriched in common biological pathways such as cell surface receptor signaling pathway and response to external stimulus. In conclusion, we demonstrated that irrespective of the pathogen type, there are common immunoregulatory and proinflammatory signals.