Host receptors: the key to establishing cells with broad viral tropism for vaccine production

Inactivation mechanism of cold plasma combined with 222 nm ultraviolet for spike protein and its application in disinfecting of SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible virus that has precipitated a worldwide pandemic of coronavirus disease since 2019. Developing an effective disinfection strategy is crucial to prevent the risk of surface cross-contamination by SARS-CoV-2. This study employed pseudovirus and the receptor-binding domain (RBD) protein of SARS-CoV-2 as models to investigate the spike protein inactivation process and its underlying mechanisms using a novel nonthermal technology. Cold plasma combined with 222 nm ultraviolet (CP+UV) treatment was applied to accelerate the generation of reactive species and enhance sterilization efficiency. The results indicated that the binding activity of RBD protein was completely inhibited at specific concentrations (0.01-0.05 mg/cm2) with corresponding treatment times of 15-30 s. The mechanism potentially involves the reactive species generated by CP+UV, which react with the spike protein RBD of SARS-CoV-2, leading to the loss of SARS-CoV-2 infectivity by causing damage to the β-sheet structure and chemical bonds in the RBD protein. Validated by a biosafety level 3 (BSL3) laboratory, the CP+UV treatment for 30 s could completely inactivate SARS-CoV-2 with a concentration of 19054 ± 1112 TCID50/cm2. Therefore, this study potentially provides a novel disinfection strategy for the inactivation of SARS-CoV-2 on surface cross-contamination.

The Host-Pathogen Interplay: A Tale of Two Stories within the Cornea and Posterior Segment

Ocular infectious diseases are an important cause of potentially preventable vision loss and blindness. In the following manuscript, we will review ocular immunology and the pathogenesis of herpesviruses and Pseudomonas aeruginosa infections of the cornea and posterior segment. We will highlight areas of future research and what is currently known to promote bench-to-bedside discoveries to improve clinical outcomes of these debilitating ocular diseases.

Targeting GBM with an Oncolytic Picornavirus SVV-001 alone and in combination with fractionated Radiation in a Novel Panel of Orthotopic PDX models

BACKGROUND

Animal models representing different molecular subtypes of glioblastoma multiforme (GBM) is desired for developing new therapies. SVV-001 is an oncolytic virus selectively targeting cancer cells. It's capacity of passing through the blood brain barrier makes is an attractive novel approach for GBM.

MATERIALS AND METHODS

23 patient tumor samples were implanted into the brains of NOD/SCID mice (1 × 105 cells/mouse). Tumor histology, gene expression (RNAseq), and growth rate of the developed patient-derived orthotopic xenograft (PDOX) models were compared with the originating patient tumors during serial subtransplantations. Anti-tumor activities of SVV-001 were examined in vivo; and therapeutic efficacy validated in vivo via single i.v. injection (1 × 1011 viral particle) with or without fractionated (2 Gy/day x 5 days) radiation followed by analysis of animal survival times, viral infection, and DNA damage.

RESULTS

PDOX formation was confirmed in 17/23 (73.9%) GBMs while maintaining key histopathological features and diffuse invasion of the patient tumors. Using differentially expressed genes, we subclassified PDOX models into proneural, classic and mesenchymal groups. Animal survival times were inversely correlated with the implanted tumor cells. SVV-001 was active in vitro by killing primary monolayer culture (4/13 models), 3D neurospheres (7/13 models) and glioma stem cells. In 2/2 models, SVV-001 infected PDOX cells in vivo without harming normal brain cells and significantly prolonged survival times in 2/2 models. When combined with radiation, SVV-001 enhanced DNA damages and further prolonged animal survival times.

CONCLUSION

A panel of 17 clinically relevant and molecularly annotated PDOX modes of GBM is developed, and SVV-001 exhibited strong anti-tumor activities in vitro and in vivo.

Viral Infection and Antiviral Treatments in Ocular Pathologies

Ocular viral infections are common and widespread globally. These infectious diseases are a major cause of acute red eyes and vision loss. The eye and its nearby tissues can be infected by several viral agents, causing infections with a short course and limited ocular implications or a long clinical progression and serious consequences for the function and structure of the ocular region. Several surveillance studies underline the increased emergence of drug resistance among pathogenic viral strains, limiting treatment options for these infections. Currently, in the event of resistant infections, topical or systemic corticosteroids are useful in the management of associated immune reactions in the eye, which contribute to ocular dysfunction. Many cases of viral eye infections are misdiagnosed as being of bacterial origin. In these cases, therapy begins late and is not targeted at the actual cause of the infection, often leading to severe ocular compromises, such as corneal infiltrates, conjunctival scarring, and reduced visual acuity. The present study aims at a better understanding of the viral pathogens that cause eye infections, along with the treatment options available.

In Silico Analysis of the Multi-Targeted Mode of Action of Ivermectin and Related Compounds

Some clinical studies have indicated activity of ivermectin, a macrocyclic lactone, against COVID-19, but a biological mechanism initially proposed for this anti-viral effect is not applicable at physiological concentrations. This in silico investigation explores potential modes of action of ivermectin and 14 related compounds, by which the infectivity and morbidity of the SARS-CoV-2 virus may be limited. Binding affinity computations were performed for these agents on several docking sites each for models of (1) the spike glycoprotein of the virus, (2) the CD147 receptor, which has been identified as a secondary attachment point for the virus, and (3) the alpha-7 nicotinic acetylcholine receptor (α7nAChr), an indicated point of viral penetration of neuronal tissue as well as an activation site for the cholinergic anti-inflammatory pathway controlled by the vagus nerve. Binding affinities were calculated for these multiple docking sites and binding modes of each compound. Our results indicate the high affinity of ivermectin, and even higher affinities for some of the other compounds evaluated, for all three of these molecular targets. These results suggest biological mechanisms by which ivermectin may limit the infectivity and morbidity of the SARS-CoV-2 virus and stimulate an α7nAChr-mediated anti-inflammatory pathway that could limit cytokine production by immune cells.

A Deadly Embrace: Hemagglutination Mediated by SARS-CoV-2 Spike Protein at Its 22 N-Glycosylation Sites, Red Blood Cell Surface Sialoglycoproteins, and Antibody

Rouleaux (stacked clumps) of red blood cells (RBCs) observed in the blood of COVID-19 patients in three studies call attention to the properties of several enveloped virus strains dating back to seminal findings of the 1940s. For COVID-19, key such properties are: (1) SARS-CoV-2 binds to RBCs in vitro and also in the blood of COVID-19 patients; (2) although ACE2 is its target for viral fusion and replication, SARS-CoV-2 initially attaches to sialic acid (SA) terminal moieties on host cell membranes via glycans on its spike protein; (3) certain enveloped viruses express hemagglutinin esterase (HE), an enzyme that releases these glycan-mediated bindings to host cells, which is expressed among betacoronaviruses in the common cold strains but not the virulent strains, SARS-CoV, SARS-CoV-2 and MERS. The arrangement and chemical composition of the glycans at the 22 N-glycosylation sites of SARS-CoV-2 spike protein and those at the sialoglycoprotein coating of RBCs allow exploration of specifics as to how virally induced RBC clumping may form. The in vitro and clinical testing of these possibilities can be sharpened by the incorporation of an existing anti-COVID-19 therapeutic that has been found in silico to competitively bind to multiple glycans on SARS-CoV-2 spike protein.

Bioinformatics analysis of rhinovirus capsid proteins VP1-4 sequences for cross-serotype vaccine development

BACKGROUND

Rhinoviruses (RV) are associated with the development and exacerbations of asthma and chronic obstructive pulmonary disease. They've also been linked to more severe diseases like pneumonia, acute bronchiolitis, croup, and otitis media. Because of the hypervariable sequences in the same serotypes, no effective vaccine against rhinoviruses has been developed to date. With the availability of new full-length genome sequences for all RV-A and RV-B serotyped strains, this study used bioinformatics to find a suitable RV strain with the highest similarity matrices to the other strains.

METHODS

The full genomic sequences of all known different RV-A and -B prototypes were downloaded from the National Centre for Biotechnology Information (NCBI) and divided into minor low-density lipoprotein receptor (LDLR) and major intercellular adhesion molecule groups (ICAM). The sequences were edited using Biological Sequence Alignment Editor, v 7.2.0 (BioEdit software) to study each capsid protein (VP1, VP2, VP3, and VP4) and analyzed using the EMBL-EBI ClustalW server and the more current Clustal Omega tool for the calculation of the identities and similarities.

RESULTS

We analyzed and predicted immunogenic motifs from capsid proteins that are conserved across distinct RV serotypes using a bioinformatics technique. The amino acid sequences of VP3 were found to be the most varied, while VP4 was the most conserved protein among all RV-A and RV-B strains. Among all strains studied, RV-74 demonstrated the highest degree of homology to other strains and could be a potential genetic source for recombinant protein production. Nine highly conserved regions with a minimum length of 9-mers were identified, which could serve as potential immune targets against rhinoviruses.

CONCLUSION

Therefore, bioinformatics analysis conducted in the current study has paved the way for the selection of immunogenic targets. Bioinformatically, the ideal strain's capsid protein is suggested to contain the most common RVs immunogenic sites.

Plasma-activated water: An alternative disinfectant for S protein inactivation to prevent SARS-CoV-2 infection

SARS-CoV-2 is a highly contagious virus and is causing a global pandemic. SARS-CoV-2 infection depends on the recognition of and binding to the cellular receptor human angiotensin-converting enzyme 2 (hACE2) through the receptor-binding domain (RBD) of the spike protein, and disruption of this process can effectively inhibit SARS-CoV-2 invasion. Plasma-activated water efficiently inactivates bacteria and bacteriophages by causing damage to biological macromolecules, but its effect on coronavirus has not been reported. In this study, pseudoviruses with the SARS-CoV-2 S protein were used as a model, and plasma-activated water (PAW) effectively inhibited pseudovirus infection through S protein inactivation. The RBD was used to study the molecular details, and the RBD binding activity was inactivated by plasma-activated water through the RBD modification. The short-lived reactive species in the PAW, such as ONOO^-, played crucial roles in this inactivation. Plasma-activated water after room-temperature storage of 30 days remained capable of significantly reducing the RBD binding with hACE2. Together, our findings provide evidence of a potent disinfection strategy to combat the epidemic caused by SARS-CoV-2.

Harness Organoid Models for Virological Studies in Animals: A Cross-Species Perspective

Animal models and cell culture in vitro are primarily used in virus and antiviral immune research. Whereas the limitation of these models to recapitulate the viral pathogenesis in humans has been made well aware, it is imperative to introduce more efficient systems to validate emerging viruses in both domestic and wild animals. Organoids ascribe to representative miniatures of organs (i.e., mini-organs), which are derived from three-dimensional culture of stem cells under respective differential conditions mimicking endogenous organogenetic niches. Organoids have broadened virological studies in the human context, particularly in recent uses for COVID19 research. This review examines the status and potential for cross-species applied organotypic culture in validating emerging animal, particularly zoonotic, viruses in domestic and wild animals.

Directed evolution in mammalian cells

Directed evolution experiments are typically carried out using in vitro systems, bacteria, or yeast-even when the goal is to probe or modulate mammalian biology. Performing directed evolution in systems that do not match the intended mammalian environment severely constrains the scope and functionality of the targets that can be evolved. We review new platforms that are now making it possible to use the mammalian cell itself as the setting for directed evolution and present an overview of frontier challenges and high-impact targets for this approach.

Targets and assay types for COVID-19 diagnosis

The lack of complete information on the immune response dynamics to infection with severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) has led to the use of mainly molecular tests such as reverse transcription PCR (RT-PCR) to diagnose Coronavirus 2019 disease (COVID-19). Although remarkable progress has been made in developing effective RT-PCR kits, the lack of specific equipment required to perform this technique in all clinical laboratories limits its widespread use. In the case of COVID-19, these tests can be used for the triage of symptomatic patients, for testing the contacts of confirmed cases, and also for the analysis and monitoring of the situation. Along with molecular tests involving reverse transcription PCR, various laboratory tests can identify the specific anti-viral antibodies or viral antigens. This review seeks to describe the targets and diagnostic methods available or currently in development for SARS-CoV-2 infection, including reverse transcription PCR (RT-PCR), serologic immunoassays (SIA) and the protein microarray method (PMM). Knowing the specific targets and the sensitivity of each assay used for COVID-19 diagnosis can lead to more efficient detection of infected patients and it can provide better management of the pandemic status.

Infection of polarized bovine respiratory epithelial cells by bovine viral diarrhea virus (BVDV)

Bovine viral diarrhea virus (BVDV) is affecting cattle populations all over the world causing acute disease, immunosuppressive effects, respiratory diseases, gastrointestinal, and reproductive failure in cattle. The virus is taken up via the oronasal route and infection of epithelial and immune cells contributes to the dissemination of the virus throughout the body. However, it is not known how the virus gets across the barrier of epithelial cells encountered in the airways. Here, we analyzed the infection of polarized primary bovine airway epithelial cells (BAEC). Infection of BAEC by a non-cytopathogenic BVDV was possible via both the apical and the basolateral plasma membrane, but the infection was most efficient when the virus was applied to the basolateral plasma membrane. Irrespective of the site of infection, BVDV was efficiently released to the apical site, while only minor amounts of virus were detected in the basal medium. This indicates that the respiratory epithelium can release large amounts of BVDV to the environment and susceptible animals via respiratory fluids and aerosols, but BVDV cannot cross the airway epithelial cells to infect subepithelial cells and establish systemic infection. Further experiments showed that the receptor, bovine CD46, for BVDV is expressed predominantly on the apical membrane domain of the polarized epithelial cells. In a CD46 blocking experiment, the addition of an antibody directed against CD46 almost completely inhibited apical infection, whereas basolateral infection was not affected. While CD46 serves as a receptor for apical infection of BAEC by BVDV, the receptor for basolateral infection remains to be elucidated.

Usage of peptidases by SARS-CoV-2 and several human coronaviruses as receptors: A mysterious story

Coronaviruses recognize a variety of host receptors to infect many humans and animals. Newly emerged severe acute respiratory syndrome coronavirus2 (SARS-CoV-2) recognizes angiotensin-converting enzyme 2 (ACE2) to gain entry into different cells. Interestingly, besides SARS-CoV2, four other human coronaviruses (HCoVs) use three different ectopeptidases (ACE2, dipeptidyl peptidase 4, and aminopeptidase N) as receptors independent of their common peptidase activity. This issue has led to the important question "why do several HCoVs rely on peptidases as their receptors?." In this paper, we discussed to answer this question. Mostly, it seems that the use of peptidases by HCoVs may be more related to their widespread presence on target cells and also viruses prefer to take advantage of molecules with relatively low affinity for their natural ligands through evolving a stronger binding affinity to the surface receptors for entry and endocytosis. Meanwhile evolutionary conservation of these receptors may allow HCoVs to switch between different host species. Finally, the choice of peptidases by HCoVs may reflect the "trial and error" nature of evolution. In conclusion, substantial efforts are needed to get a strong picture of this fascinating question and poorly explored area. Detailed understanding of the entry mechanisms offers opportunities for the development of refined strategies to stop viruses.

Expanding virus susceptibility spectrum of MDBK cells by expressing host receptors nectin 4 and TfR

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This study provides the first evidence to the previously proposed theoretical guidance for artificial cell adaptation via genomic modulation;This study contributes to the goal of broadening the permissiveness of a given cell line to viruses for massive vaccine production;This study offers a genetic modulation platform that can be easily tuned for other use.

Cell-based vaccine manufacturing is a flexible and cost-effective approach for vaccine production which, however, requires cell adaptation to new vaccine strains. Generating one omnipotent or semi-omnipotent cell line feasible for the production of multiple viruses could help resolve this problem. We previously proposed virus Baltimore subtyping-based choice of receptors and a panel of minimally preferred receptors for the establishment of cells with a broad virus susceptibility spectrum. With the aim of establishing cells sensitive to viruses of livestocks including bovine, ovine and canine, we selected TfR and Nectin 4 from the minimally preferred receptor panel, and successfully sensitized the starting cell line MDBK to CPV and CDV infection. Our study is a preliminary validation of our previously identified associations between host receptor usage and virus Baltimore subtyping. Evidence from more viruses of the same Baltimore subtyping and more starting cell lines need to be used to consolidate our results.

Emerging Pandemic Diseases: How We Got to COVID-19

Infectious diseases prevalent in humans and animals are caused by pathogens that once emerged from other animal hosts. In addition to these established infections, new infectious diseases periodically emerge. In extreme cases they may cause pandemics such as COVID-19; in other cases, dead-end infections or smaller epidemics result. Established diseases may also re-emerge, for example by extending geographically or by becoming more transmissible or more pathogenic. Disease emergence reflects dynamic balances and imbalances, within complex globally distributed ecosystems comprising humans, animals, pathogens, and the environment. Understanding these variables is a necessary step in controlling future devastating disease emergences.

Future antiviral surfaces: Lessons from COVID-19 pandemic

It is an urgent priority for advanced materials researchers to help find solutions to eliminate the COVID-19 pandemic. The transmission of the SARS-CoV-2 coronavirus is majorly through touching the contaminated surfaces and then the vulnerable mouth and eyes besides the direct contact with the infected person. This lesson inspired us to propose a strategy from the view of materials scientists on designing effective antiviral surfaces to prevent the transmission of infectious coronaviruses by disrupting their survival on various surfaces. In this perspective, based on current progress in antiviral and antibacterial coatings, we put forward some general principles for designing effective antiviral surfaces by applying natural viral inhibitors, physical/chemical modifications, and bioinspired patterns, with the mechanisms of direct disinfection, indirect disinfection, and receptor inactivation. This work maps possible solutions to inactivate the receptors of the coronavirus spikes and resist the transmission of the COVID-19 and other infectious diseases, and contribute to the prevention of future outbreaks and control of epidemics.