Coronavirus envelope protein: current knowledge

Structure and function of SARS-CoV and SARS-CoV-2 main proteases and their inhibition: A comprehensive review

Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) identified in 2003 infected ∼8000 people in 26 countries with 800 deaths, which was soon contained and eradicated by syndromic surveillance and enhanced quarantine. A closely related coronavirus SARS-CoV-2, the causative agent of COVID-19 identified in 2019, has been dramatically more contagious and catastrophic. It has infected and caused various flu-like symptoms of billions of people in >200 countries, including >6 million people died of or with the virus. Despite the availability of several vaccines and antiviral drugs against SARS-CoV-2, finding new therapeutics is needed because of viral evolution and a possible emerging coronavirus in the future. The main protease (Mpro) of these coronaviruses plays important roles in their life cycle and is essential for the viral replication. This article represents a comprehensive review of the function, structure and inhibition of SARS-CoV and -CoV-2 Mpro, including structure-activity relationships, protein-inhibitor interactions and clinical trial status.

Natural products as potential lead compounds to develop new antiviral drugs over the past decade

Virus infection has been one of the main causes of human death since the ancient times. Even though more and more antiviral drugs have been approved in clinic, long-term use can easily lead to the emergence of drug resistance and side effects. Fortunately, there are many kinds of metabolites which were produced by plants, marine organisms and microorganisms in nature with rich structural skeletons, and they are natural treasure house for people to find antiviral active substances. Aiming at many types of viruses that had caused serious harm to human health in recent years, this review summarizes the natural products with antiviral activity that had been reported for the first time in the past ten years, we also sort out the source, chemical structure and safety indicators in order to provide potential lead compounds for the research and development of new antiviral drugs.

Mapping the Lipid Signatures in COVID-19 Infection: Diagnostic and Therapeutic Solutions

The COVID-19 pandemic ignited research centered around the identification of robust biomarkers and therapeutic targets. SARS-CoV-2, the virus responsible, hijacks the metabolic machinery of the host cells. It relies on lipids and lipoproteins of host cells for entry, trafficking, immune evasion, viral replication, and exocytosis. The infection causes host cell lipid metabolic remodelling. Targeting lipid-based processes is thus a promising strategy for countering COVID-19. Here, we review the role of lipids in the different steps of the SARS-CoV-2 pathogenesis and identify lipid-centric targetable avenues. We discuss lipidome changes in infected patients and their relevance as potential clinical diagnostic or prognostic biomarkers. We summarize the emerging direct and indirect therapeutic approaches for targeting COVID-19 using lipid-inspired approaches. Given that viral protein-targeted therapies may become less effective due to mutations in emerging SARS-CoV-2 variants, lipid-inspired interventions may provide additional and perhaps better means of combating this and future pandemics.

Targeting Viral ORF3a Protein: A New Approach to Mitigate COVID-19 Induced Immune Cell Apoptosis and Associated Respiratory Complications

Infection with SARS-CoV-2 is a growing concern to the global well-being of the public at present. Different amino acid mutations alter the biological and epidemiological characteristics, as well as immune resistance of SARS-CoV-2. The virus-induced pulmonary impairment and inflammatory cytokine storm are directly related to its clinical manifestations. But, the fundamental mechanisms of inflammatory responses are found to be the reason for the death of immune cells which render the host immune system failure. Apoptosis of immune cells is one of the most common forms of programmed cell death induced by the virus for its survival and virulence property. ORF3a, a SARS-CoV-2 accessory viral protein, induces apoptosis in host cells and suppress the defense mechanism. This suggests, inhibiting SARS-CoV-2 ORF3a protein is a good therapeutic strategy for the treatment in COVID-19 infection by promoting the host immune defense mechanism.

Association of Ambient Temperature and Absolute Humidity with the Effective Reproduction Number of COVID-19 in Japan

This study aimed to quantify the exposure-lag-response relationship between short-term changes in ambient temperature and absolute humidity and the transmission dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Japan. The prefecture-specific daily time-series of newly confirmed cases, meteorological variables, retail and recreation mobility, and Government Stringency Index were collected for all 47 prefectures of Japan for the study period from 15 February 2020 to 15 October 2022. Generalized conditional Gamma regression models were formulated with distributed lag nonlinear models by adopting the case-time-series design to assess the independent and interactive effects of ambient temperature and absolute humidity on the relative risk (RR) of the time-varying effective reproductive number (Rt). With reference to 17.8 °C, the corresponding cumulative RRs (95% confidence interval) at a mean ambient temperatures of 5.1 °C and 27.9 °C were 1.027 (1.016-1.038) and 0.982 (0.974-0.989), respectively, whereas those at an absolute humidity of 4.2 m/g3 and 20.6 m/g3 were 1.026 (1.017-1.036) and 0.995 (0.985-1.006), respectively, with reference to 10.6 m/g3. Both extremely hot and humid conditions synergistically and slightly reduced the Rt. Our findings provide a better understanding of how meteorological drivers shape the complex heterogeneous dynamics of SARS-CoV-2 in Japan.

Identification of potential SLA-I-specific T-cell epitopes within the structural proteins of porcine deltacoronavirus

Porcine deltacoronavirus (PDCoV) is an emerging swine enteropathogenic coronavirus that mainly threatens newborn piglets and poses a potential broad cross-species transmission risk. The antigenic epitopes of PDCoV are currently unidentified, and no information about T cell epitopes is available. Here, T-cell epitopes of PDCoV structural proteins were predicted using computational methods. 17 epitope peptides were synthesized and then screened using ELIspot, intracellular cytokine staining (ICS), and RT-qPCR detection of IFN-γ mRNA to evaluate their ability to elicit interferon-gamma (IFN-γ) responses in peripheral blood mononuclear cells (PBMCs) from PDCoV-challenged pigs. Five peptides (M1, M2, M3, N6, and S4) elicited high levels of IFN-γ and were investigated further as potential T-cell epitope candidates. All five peptides were cytotoxic T lymphocyte (CTL) epitopes, and two peptides (M3, N6) were recognized simultaneously by CD8 + and CD4 + T cells. A multi-epitope peptide combining the five epitopes (designated "5T") was synthesized and its immune response and protection efficacy was evaluated in a piglet model. ELISpot assay results indicated that 5T induces robust epitope-specific cellular immune responses. Four epitopes (M1, M2, N6, S4) elicited IFN-γ responses in 5T-vaccinated piglets. No obvious protection efficacy was detected in piglets vaccinated with 5T alone. Our results provide valuable information concerning PDCoV-related antigenic epitopes and will be useful in the design of epitope-based vaccines.

Distinct motifs in the E protein are required for SARS-CoV-2 virus particle formation and lysosomal deacidification in host cells

IMPORTANCE

Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), has caused a global public health crisis. The E protein, a structural protein found in this virus particle, is also known to be a viroporin. As such, it forms oligomeric ion channels or pores in the host cell membrane. However, the relationship between these two functions is poorly understood. In this study, we showed that the roles of E protein in virus particle and viroporin formation are distinct. This study contributes to the development of drugs that inhibit SARS-CoV-2 virus particle formation. Additionally, we designed a highly sensitive and high-throughput virus-like particle detection system using the HiBiT tag, which is a useful tool for studying the release of SARS-CoV-2.

A comparative analysis of the partitioning behaviour of SARS-CoV-2 RNA in liquid and solid fractions of wastewater

As fragments of SARS-CoV-2 RNA can be quantified and measured temporally in wastewater, surveillance of concentrations of SARS-CoV-2 in wastewater has become a vital resource for tracking the spread of COVID-19 in and among communities. However, the absence of standardized methods has affected the interpretation of data for public health efforts. In particular, analyzing either the liquid or solid fraction has implications for the interpretation of how viral RNA is quantified. Characterizing how SARS-CoV-2 or its RNA fragments partition in wastewater is a central part of understanding fate and behaviour in wastewater. In this study, partitioning of SARS-CoV-2 was investigated by use of centrifugation with varied durations of spin and centrifugal force, polyethylene glycol (PEG) precipitation followed by centrifugation, and ultrafiltration of wastewater. Partitioning of the endogenous pepper mild mottled virus (PMMoV), used to normalize the SARS-CoV-2 signal for fecal load in trend analysis, was also examined. Additionally, two surrogates for coronavirus, human coronavirus 229E and murine hepatitis virus, were analyzed as process controls. Even though SARS-CoV-2 has an affinity for solids, the total RNA copies of SARS-CoV-2 per wastewater sample, after centrifugation (12,000 g, 1.5 h, no brake), were partitioned evenly between the liquid and solid fractions. Centrifugation at greater speeds for longer durations resulted in a shift in partitioning for all viruses toward the solid fraction except for PMMoV, which remained mostly in the liquid fraction. The surrogates more closely reflected the partitioning of SARS-CoV-2 under high centrifugation speed and duration while PMMoV did not. Interestingly, ultrafiltration devices were inconsistent in estimating RNA copies in wastewater, which can influence the interpretation of partitioning. Developing a better understanding of the fate of SARS-CoV-2 in wastewater and creating a foundation of best practices is the key to supporting the current pandemic response and preparing for future potential infectious diseases.

Atomic structure of the open SARS-CoV-2 E viroporin

The envelope (E) protein of the SARS-CoV-2 virus forms cation-conducting channels in the endoplasmic reticulum Golgi intermediate compartment (ERGIC) of infected cells. The calcium channel activity of E is associated with the inflammatory responses of COVID-19. Using solid-state NMR (ssNMR) spectroscopy, we have determined the open-state structure of E's transmembrane domain (ETM) in lipid bilayers. Compared to the closed state, open ETM has an expansive water-filled amino-terminal chamber capped by key glutamate and threonine residues, a loose phenylalanine aromatic belt in the middle, and a constricted polar carboxyl-terminal pore filled with an arginine and a threonine residue. This structure gives insights into how protons and calcium ions are selected by ETM and how they permeate across the hydrophobic gate of this viroporin.

Cryo-electron microscopy in the fight against COVID-19-mechanism of virus entry

Cryogenic electron microscopy (cryo-EM) and electron tomography (cryo-ET) have become a critical tool for studying viral particles. Cryo-EM has enhanced our understanding of viral assembly and replication processes at a molecular resolution. Meanwhile, in situ cryo-ET has been used to investigate how viruses attach to and invade host cells. These advances have significantly contributed to our knowledge of viral biology. Particularly, prompt elucidations of structures of the SARS-CoV-2 spike protein and its variants have directly impacted the development of vaccines and therapeutic measures. This review discusses the progress made by cryo-EM based technologies in comprehending the severe acute respiratory syndrome coronavirus-2 (SARS-Cov-2), the virus responsible for the devastating global COVID-19 pandemic in 2020 with focus on the SARS-CoV-2 spike protein and the mechanisms of the virus entry and replication.

Virtual screening and molecular dynamics simulation study of abyssomicins as potential inhibitors of COVID-19 virus main protease and spike protein

The lack of any effective cure for the infectious COVID-19 disease has created a sense of urgency and motivated the search for effective antiviral drugs. Abyssomicins are actinomyces-derived spirotetronates polyketides antibiotics known for their promising antibacterial, antitumor, and antiviral activities. In this study, computational approaches were used to investigate the binding mechanism and the inhibitory ability of 38 abyssomicins against the main protease (Mpro) and the spike protein receptor-binding domain (RBD) of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The results identified abyssomicins C, J, W, atrop-O-benzyl abyssomicin C, and atrop-O-benzyl desmethyl abyssomicin C as the most potential inhibitors of Mpro and RBD with binding energy ranges between -8.1 and -9.9 kcal mol-1; and between -6.9 and -8.2 kcal mol-1, respectively. Further analyses of physicochemical properties and drug-likeness suggested that all selected active abyssomicins, with the exception of abyssomicin J, obeyed Lipinski's rule of five. The stability of protein-ligand complexes was confirmed by performing molecular dynamics simulation for 100 ns and evaluating parameters such as such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), total number of contacts, and secondary structure. Prime/MM-GBSA (Molecular Mechanics-General Born Surface Area) and principal component analysis (PCA) analyses also confirmed the stable nature of protein-ligand complexes. Overall, the results showed that the studied abyssomicins have significant interactions with the selected protein targets; therefore, they were deemed viable candidates for further in vitro and in vivo evaluation.Communicated by Ramaswamy H. Sarma.

Incorporating MOOC and COVID-19-Related Scientific Papers into Veterinary Microbiology Teaching to Enhance Students' Learning Performance and Professional Recognition

The COVID-19 pandemic has exerted a huge adverse influence on global teaching activities and students' psychological status. Veterinary microbiology is mainly concerned with bacterial and viral diseases, including coronavirus diseases. An innovative online-to-offline teaching approach for this course was established to stimulate students' learning initiative and mitigate their anxiety about COVID-19. A well-established massive open online course (MOOC) was first adopted as preview material before class, followed by in-person teaching. Additionally, COVID-19-related scientific papers were used as pre-class reading material in veterinary microbiology and were further explained in class. The effect of this innovative teaching mode was systematically evaluated by final examination scores and questionnaires. The average score (81.75) and excellence score rating (> 85 scores, 37.3%) resulting from this blended teaching mode were not statistically higher than those of the online-only (79.19, p = .115; 28.6%, p = .317) or offline-only (79.47, p = .151; 27.9%, p = .269) teaching modes. This may be due to the sample size investigated; however, the results indicate that the innovative teaching mode did not decrease teaching quality. Additionally, most subjects (72.9%) were satisfied with the blended mode and supported its future use. Intriguingly, the introduction of COVID-19-related scientific papers helped students understand virology, relieve their anxiety, and increase their professional identity. Collectively, the innovative approach to teaching veterinary microbiology in this study provides a beneficial reference for other teachers to maintain and improve teaching quality.

COVID-19 and Gastrointestinal Tract: From Pathophysiology to Clinical Manifestations

Background: Since its first report in Wuhan, China, in December 2019, COVID-19 has become a pandemic, affecting millions of people worldwide. Although the virus primarily affects the respiratory tract, gastrointestinal symptoms are also common. The aim of this narrative review is to provide an overview of the pathophysiology and clinical manifestations of gastrointestinal COVID-19. Methods: We conducted a systematic electronic search of English literature up to January 2023 using Medline, Scopus, and the Cochrane Library, focusing on papers that analyzed the role of SARS-CoV-2 in the gastrointestinal tract. Results: Our review highlights that SARS-CoV-2 directly infects the gastrointestinal tract and can cause symptoms such as diarrhea, nausea/vomiting, abdominal pain, anorexia, loss of taste, and increased liver enzymes. These symptoms result from mucosal barrier damage, inflammation, and changes in the microbiota composition. The exact mechanism of how the virus overcomes the acid gastric environment and leads to the intestinal damage is still being studied. Conclusions: Although vaccination has increased the prevalence of less severe symptoms, the long-term interaction with SARS-CoV-2 remains a concern. Understanding the interplay between SARS-CoV-2 and the gastrointestinal tract is essential for future management of the virus.

Potent multi-target natural inhibitors against SARS-CoV-2 from medicinal plants of the Himalaya: a discovery from hybrid machine learning, chemoinformatics, and simulation assisted screening

The emergence and immune evasion ability of SARS-CoV-2 Omicron strains, mainly BA.5.2 and BF.7 and other variants of concern have raised global apprehensions. With this context, the discovery of multitarget inhibitors may be proven more comprehensive paradigm than its one-drug-to-one target counterpart. In the current study, a library of 271 phytochemicals from 25 medicinal plants from the Indian Himalayan Region has been virtually screened against SARS-CoV-2 by targeting nine virus proteins, viz., papain-like protease, main protease, nsp12, helicase, nsp14, nsp15, nsp16, envelope, and nucleocapsid for screening of a multi-target inhibitor against the viral replication. Initially, 94 phytochemicals were screened by a hybrid machine learning model constructed by combining 6 confirmatory bioassays against SARS-CoV-2 replication using an instance-based learner lazy k-nearest neighbour classifier. Further, 25 screened compounds with excellent drug-like properties were subjected to molecular docking. The phytochemical Cepharadione A from the plant Piper longum showed binding potential against four proteins with the highest binding energy of -10.90 kcal/mol. The compound has acceptable absorption, distribution, metabolism, excretion, and toxicity properties and exhibits stable binding behaviour in terms of root mean square deviation (0.068 ± 0.05 nm), root-mean-square fluctuation, hydrogen bonds, solvent accessible surface area (83.88-161.89 nm2), and molecular mechanics Poisson-Boltzmann surface area during molecular dynamics simulation of 200 ns with selected target proteins. Concerning the utility of natural compounds in the therapeutics formulation, Cepharadione A could be further investigated as a remarkable lead candidate for the development of therapeutic drugs against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

The Key Site Variation and Immune Challenges in SARS-CoV-2 Evolution

Coronavirus disease 2019 (COVID-19) is a worldwide public health and economic threat, and virus variation amplifies the difficulty in epidemic prevention and control. The structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been studied extensively and is now well defined. The S protein is the most distinguishing feature in terms of infection and immunity, mediating virus entrance and inducing neutralizing antibodies. The S protein and its essential components are also the most promising target to develop vaccines and antibody-based drugs. Therefore, the key site mutation in the S gene is of high interest. Among them, RBD, NTD, and furin cleavage sites are the most mutable regions with the most mutation sites and the most serious consequences for SARS-CoV-2 biological characteristics, including infectivity, pathogenicity, natural immunity, vaccine efficacy, and antibody therapeutics. We are also aware that this outbreak may not be the last. Therefore, in this narrative review, we summarized viral variation and prevalence condition, discussed specific amino acid replacement and associated immune challenges and attempted to sum up some prevention and control strategies by reviewing the literature on previously published research about SARS-CoV-2 variation to assist in clarifying the mutation pathway and consequences of SARS-CoV-2 for developing countermeasures against such viruses as soon as possible.

Arbidol increases the survival rate by mitigating inflammation in suckling mice infected with human coronavirus OC43 virus

Human coronavirus OC43 (HCoV-OC43) often causes common cold and is able to neuroinvasive, but it can also induce lower respiratory tract infections (LRTI) especially in children and the elderly adults with underlying diseases. HCoV-OC43 infections currently have no approved antiviral treatment. Arbidol (ARB) is a broad-spectrum antiviral and is an antiviral medication for the treatment of influenza used in Russia and China. Due to its multiple mechanisms of action, such as inhibition of viral fusion and entry, immunomodulation, and modulation of host cell signaling pathways, ARB has the potential to be an effective treatment option for viral infections. Therefore, the study aims to investigate the activities of ARB against HCoV-OC43 infections. Suckling mice were infected with HCoV-OC43 and treated with ARB (50, 25 and 12.5 mg/kg/d) by gavage once daily for 4 days. the survival rates and body weight were recorded, the viral titer was measured by real-time quantitative polymerase chain reaction, cytokine levels were measured by Bio-Plex assays. Histopathological changes of the lungs and brain were analyzed. Our results show ARB increased the survival rate, reduced viral copy numbers in the lung, mitigated pro-inflammatory cytokine production, and improved brain and lung histopathology significantly without any significant toxicity or side effects in vivo. Our results suggest ARB could be a promising approach for the prevention and treatment of HCoV-OC43 while further studies are needed to address these possibilities and the underlying mechanism.

Regulating Select Agent Chimeras: Defining the Problem(s) Through the Lens of SARS-CoV-1/SARS-CoV-2 Chimeric Viruses

In late 2021, the US Centers for Disease Control and Prevention (CDC) posted an interim final rule (86 FR 64075) to the federal register regulating the possession, use, and transfer of SARS-CoV-1/SARS-CoV-2 chimeric viruses. In doing so, the CDC provided the reasoning that viral chimeras combining the transmissibility of SARS-CoV-2 with the pathogenicity and lethality of SARS-CoV-1 pose a significant risk to public health and should thus be placed on the select agents and toxins list. However, 86 FR 64075 lacked clarity in its definitions and scope, some of which the CDC addressed in response to public comments in the final rule, 88 FR 13322, in early 2023. To evaluate these regulatory actions, we reviewed the existing select agent regulations to understand the landscape of chimeric virus regulation. Based on our findings, we first present clear definitions for the terms "chimeric virus," "viral chimera," and "virulence factor" and provide a list of SARS-CoV-1 virulence factors in an effort to aid researchers and federal rulemaking for these agents moving forward. We then provide suggestions for a combination of similarity and functional characteristic cutoffs that the government could use to enable researchers to distinguish between regulated and nonregulated chimeras. Finally, we discuss current select agent regulations and their overlaps with 86 FR 64075 and 88 FR 13322 and make suggestions for how to address chimera concerns within and/or without these regulations. Collectively, we believe that our findings fill important gaps in current federal regulations and provide forward-looking philosophical and practical analysis that can guide future decisionmaking.

SARS-CoV-2 prevalence in domestic and wildlife animals: A genomic and docking based structural comprehensive review

The SARS-CoV-2 virus has been identified as the infectious agent that led to the COVID-19 pandemic, which the world has seen very recently. Researchers have linked the SARS-CoV-2 outbreak to bats for the zoonotic spread of the virus to humans. Coronaviruses have a crown-like shape and positive-sense RNA nucleic acid. It attaches its spike glycoprotein to the host angiotensin-converting enzyme 2 (ACE2) receptor. Coronavirus genome comprises 14 ORFs and 27 proteins, spike glycoprotein being one of the most critical proteins for viral pathogenesis. Many mammals and reptiles, including bats, pangolins, ferrets, snakes, and turtles, serve as the principal reservoirs for this virus. But many experimental investigations have shown that certain domestic animals, including pigs, chickens, dogs, cats, and others, may also be able to harbor this virus, whether they exhibit any symptoms. These animals act as reservoirs for SARS-CoV, facilitating its zoonotic cross-species transmission to other species, including humans. In this review, we performed a phylogenetic analysis with multiple sequence alignment and pairwise evolutionary distance analysis, which revealed the similarity of ACE2 receptors in humans, chimpanzees, domestic rabbits, house mice, and golden hamsters. Pairwise RMSD analysis of the spike protein from some commonly reported SARS-CoV revealed that bat and pangolin coronavirus shared the highest structural similarity with human coronavirus. In a further experiment, molecular docking confirmed a higher affinity of pig, bat, and pangolin coronavirus spike proteins' affinity to the human ACE2 receptor. Such comprehensive structural and genomic analysis can help us to forecast the next likely animal source of these coronaviruses that may infect humans. To combat these zoonotic illnesses, we need a one health strategy that considers the well-being of people and animals and the local ecosystem.

Simultaneous Detection of SARS-CoV-2 Nucleoprotein and Receptor Binding Domain by a Multi-Area Reflectance Spectroscopy Sensor

The COVID-19 pandemic has emphasized the urgent need for point-of-care methods suitable for the rapid and reliable diagnosis of viral infections. To address this demand, we report the rapid, label-free simultaneous determination of two SARS-CoV-2 proteins, namely, the nucleoprotein and the receptor binding domain peptide of S1 protein, by implementing a bioanalytical device based on Multi Area Reflectance Spectroscopy. Simultaneous detection of these two proteins is achieved by using silicon chips with adjacent areas of different silicon dioxide thickness on top, each of which is modified with an antibody specific to either the nucleoprotein or the receptor binding domain of SARS-CoV-2. Both areas were illuminated by a single probe that also collected the reflected light, directing it to a spectrometer. The online conversion of the combined reflection spectra from the two silicon dioxide areas into the respective adlayer thickness enabled real-time monitoring of immunoreactions taking place on the two areas. Several antibodies have been tested to define the pair, providing the higher specific signal following a non-competitive immunoassay format. Biotinylated secondary antibodies and streptavidin were used to enhance the specific signal. Both proteins were detected in less than 12 min, with detection limits of 1.0 ng/mL. The assays demonstrated high repeatability with intra- and inter-assay coefficients of variation lower than 10%. Moreover, the recovery of both proteins from spiked samples prepared in extraction buffer from a commercial self-test kit for SARS-CoV-2 collection from nasopharyngeal swabs ranged from 90.0 to 110%. The short assay duration in combination with the excellent analytical performance and the compact instrument size render the proposed device and assay suitable for point-of-care applications.

Neurological complications and effects of COVID-19: Symptoms and conceivable mechanisms

A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in December 2019 in Wuhan, China. The new coronavirus disease (COVID-19) was declared a global pandemic by the World Health Organization (WHO) in March 2020. SARS-CoV-2 can invade the nervous system aside from infecting the respiratory system as its primary target. The most common nervous system symptoms of COVID-19 are stated as headache, myalgia, fatigue, nausea, vomiting, sudden and unexplained anosmia, and ageusia. More severe conditions such as encephalomyelitis, acute myelitis, thromboembolic events, ischemic stroke, intracerebral hemorrhage, Guillain-Barré-syndrome, Bell's palsy, rhabdomyolysis, and even coma have also been reported. Cohort studies revealed that neurological findings are associated with higher morbidity and mortality. The neurological symptoms and manifestations caused by SARS-CoV-2 and COVID-19 are examined and summarized in this article.

Nano-based techniques: A revolutionary approach to prevent covid-19 and enhancing human awareness

In every century of history, there are many new diseases emerged, which are not even cured by many developed countries. Today, despite of scientific development, new deadly pandemic diseases are caused by microorganisms. Hygiene is considered to be one of the best methods of avoiding such communicable diseases, especially viral diseases. Illness caused by SARS-CoV-2 was termed COVID-19 by the WHO, the acronym derived from "coronavirus disease 2019. The globe is living in the worst epidemic era, with the highest infection and mortality rate owing to COVID-19 reaching 6.89% (data up to March 2023). In recent years, nano biotechnology has become a promising and visible field of nanotechnology. Interestingly, nanotechnology is being used to cure many ailments and it has revolutionized many aspects of our lives. Several COVID-19 diagnostic approaches based on nanomaterial have been developed. The various metal NPs, it is highly anticipated that could be viable and economical alternatives for treating drug resistant in many deadly pandemic diseases in near future. This review focuses on an overview of nanotechnology's increasing involvement in the diagnosis, prevention, and therapy of COVID-19, also this review provides readers with an awareness and knowledge of importance of hygiene.

An overview on medicinal plants used for combating coronavirus: Current potentials and challenges

Worldwide, Severe acute respiratory syndrome Coronavirus (SARS-CoV-2) pandemic crisis, causing many morbidities, mortality, and devastating impact on economies, so the current outbreak of the CoV-2 is a major concern for global health. The infection spread quickly and caused chaos in many countries around the world. The slow discovery of CoV-2 and the limited treatment options are among the main challenges. Therefore, the development of a drug that is safe and effective against CoV-2 is urgently needed. The present overview briefly summarizes CoV-2 drug targets ex: RNA-dependent RNA polymerase (RdRp), papain-like protease (PLpro), 3-chymotrypsin-like protease (3CLpro), transmembrane serine protease enzymes (TMPRSS2), angiotensin-converting enzyme 2 (ACE2), structural protein (N, S, E, and M), and virulence factors (NSP1, ORF7a, and NSP3c) for which drug design perspective can be considered. In addition, summarize all anti-COVID-19 medicinal plants and phytocompounds and their mechanisms of action to be used as a guide for further studies.

Simultaneous Profiling of Palmitoylomics and Glycomics with Photo/pH Dual-Responsive Magnetic Nanocomposites

Following an in-depth examination of a single type of protein posttranslational modification, the synergistic analysis of two or more modification types has gradually emerged as a focal point in proteomic research. Palmitoylation and glycosylation are both critical for protein, implicated in carcinogenesis and inflammation. In this study, novel dual-responsive magnetic nanocomposites that serve as an ideal platform for the sequential or simultaneous enrichment of palmitoyl and glycopeptides are reported. The nanocomposites denoted as magDVS-VBA are constructed by modifying magnetic nanoparticles with azobenzene and divinyl sulfone (DVS), and self-assembled with 4-vinylbenzeneboronic acid (VBA)-immobilized β-cyclodextrin, which responds to light. The incorporated DVS component possesses the ability to recognize palmitoyl or glycopeptides under different pH conditions, whereas the introduction of VBA enhances the affinity of the nanocomposite for glycopeptides. Notably, magDVS-VBA exhibits flexible photo-, pH-, and magnetic-responsive capabilities, enabling the simultaneous recognition of hydrophobic palmitoyl peptides and hydrophilic glycopeptides for the first time. The developed platform demonstrates high specificity for sensitive palmitoylomics and glycomics analysis of mouse liver tissue, providing an effective method for studying of their crosstalk, and potential implications in clinical applications.

Analysis of SARS-CoV-2 interactions with the Vero cell lines by scanning electron microscopy

In this study, scanning electron microscopy (SEM) was used to study the cell structure of SARS-CoV-2 infected cells. Our measurements revealed infection remodeling caused by infection, including the emergence of new specialized areas where viral morphogenesis occurs at the cell membrane. Intercellular extensions for viral cell surfing have also been observed. Our results expand knowledge of SARS-CoV-2 interactions with cells, its spread from cell to cell, and their size distribution. Our findings suggest that SEM is a useful microscopic method for intracellular ultrastructure analysis of cells exhibiting specific surface modifications that could also be applied to studying other important biological processes.

Rapid Determination of the Topology of Oligomeric α-Helical Membrane Proteins by Water- and Lipid-Edited Methyl NMR

Single-span oligomeric α-helical transmembrane proteins are common in virus ion channels, which are targets of antiviral drugs. Knowledge about the high-resolution structures of these oligomeric α-helical bundles is so far scarce. Structure determination of these membrane proteins by solid-state NMR traditionally requires resolving and assigning protein chemical shifts and measuring many interhelical distances, which are time-consuming. To accelerate experimental structure determination, here we introduce a simple solid-state NMR approach that uses magnetization transfer from water and lipid protons to the protein. By detecting the water- and lipid-transferred intensities of the high-sensitivity methyl 13C signals of Leu, Val, and Ile residues, which are highly enriched in these membrane proteins, we can derive models of the topology of these homo-oligomeric helical bundles. The topology is specified by the positions of amino acid residues in heptad repeats and the orientations of residues relative to the channel pore, lipids, and the helical interface. We demonstrate this water- and lipid-edited methyl NMR approach on the envelope (E) protein of SARS-CoV-2, the causative agent of the COVID-19 pandemic. We show that water-edited and lipid-edited 2D 13C-13C correlation spectra can be measured with sufficient sensitivity. Even without resolving multiple residues of the same type in the NMR spectra, we can obtain the helical bundle topology. We apply these experiments to the structurally unknown E proteins of the MERS coronavirus and the human coronavirus NL63. The resulting structural topologies show interesting differences in the positions of the aromatic residues in these three E proteins, suggesting that these viroporins may have different mechanisms of activation and ion conduction.

CD36 mediates SARS-CoV-2-envelope-protein-induced platelet activation and thrombosis

Aberrant coagulation and thrombosis are associated with severe COVID-19 post-SARS-CoV-2 infection, yet the underlying mechanism remains obscure. Here we show that serum levels of SARS-CoV-2 envelope (E) protein are associated with coagulation disorders of COVID-19 patients, and intravenous administration of the E protein is able to potentiate thrombosis in mice. Through protein pull-down and mass spectrometry, we find that CD36, a transmembrane glycoprotein, directly binds with E protein and mediates hyperactivation of human and mouse platelets through the p38 MAPK-NF-κB signaling pathway. Conversely, the pharmacological blockade of CD36 or p38 notably attenuates human platelet activation induced by the E protein. Similarly, the genetic deficiency of CD36, as well as the pharmacological inhibition of p38 in mice, significantly diminishes E protein-induced platelet activation and thrombotic events. Together, our study reveals a critical role for the CD36-p38 axis in E protein-induced platelet hyperactivity, which could serve as an actionable target for developing therapies against aberrant thrombotic events related to the severity and mortality of COVID-19.

Polypharmacology guided drug repositioning approach for SARS-CoV2

Drug repurposing has emerged as an important strategy and it has a great potential in identifying therapeutic applications for COVID-19. An extensive virtual screening of 4193 FDA approved drugs has been carried out against 24 proteins of SARS-CoV2 (NSP1-10 and NSP12-16, envelope, membrane, nucleoprotein, spike, ORF3a, ORF6, ORF7a, ORF8, and ORF9b). The drugs were classified into top 10 and bottom 10 drugs based on the docking scores followed by the distribution of their therapeutic indications. As a result, the top 10 drugs were found to have therapeutic indications for cancer, pain, neurological disorders, and viral and bacterial diseases. As drug resistance is one of the major challenges in antiviral drug discovery, polypharmacology and network pharmacology approaches were employed in the study to identify drugs interacting with multiple targets and drugs such as dihydroergotamine, ergotamine, bisdequalinium chloride, midostaurin, temoporfin, tirilazad, and venetoclax were identified among the multi-targeting drugs. Further, a pathway analysis of the genes related to the multi-targeting drugs was carried which provides insight into the mechanism of drugs and identifying targetable genes and biological pathways involved in SARS-CoV2.

Recent Advances in Quantum Dot-Based Lateral Flow Immunoassays for the Rapid, Point-of-Care Diagnosis of COVID-19

The COVID-19 pandemic has spurred demand for efficient and rapid diagnostic tools that can be deployed at point of care to quickly identify infected individuals. Existing detection methods are time consuming and they lack sensitivity. Point-of-care testing (POCT) has emerged as a promising alternative due to its user-friendliness, rapidity, and high specificity and sensitivity. Such tests can be conveniently conducted at the patient's bedside. Immunodiagnostic methods that offer the rapid identification of positive cases are urgently required. Quantum dots (QDs), known for their multimodal properties, have shown potential in terms of combating or inhibiting the COVID-19 virus. When coupled with specific antibodies, QDs enable the highly sensitive detection of viral antigens in patient samples. Conventional lateral flow immunoassays (LFAs) have been widely used for diagnostic testing due to their simplicity, low cost, and portability. However, they often lack the sensitivity required to accurately detect low viral loads. Quantum dot (QD)-based lateral flow immunoassays have emerged as a promising alternative, offering significant advancements in sensitivity and specificity. Moreover, the lateral flow immunoassay (LFIA) method, which fulfils POCT standards, has gained popularity in diagnosing COVID-19. This review focuses on recent advancements in QD-based LFIA for rapid POCT COVID-19 diagnosis. Strategies to enhance sensitivity using QDs are explored, and the underlying principles of LFIA are elucidated. The benefits of using the QD-based LFIA as a POCT method are highlighted, and its published performance in COVID-19 diagnostics is examined. Overall, the integration of quantum dots with LFIA holds immense promise in terms of revolutionizing COVID-19 detection, treatment, and prevention, offering a convenient and effective approach to combat the pandemic.

The Portuguese Public Hospitals Performance Evolution before and during the SARS-CoV-2 Pandemic (2017–2022)

COVID-19 is a disease caused by SARS-CoV-2, which has spread worldwide since the beginning of 2020. Several pharmaceutical and non-pharmaceutical strategies were proposed to contain the virus, including vaccination and lockdowns. One of the consequences of the pandemic was the denial or delay of access to convenient healthcare services, but also potentially the increase in adverse events within those services, like the number of hospital infections. Therefore, the main question here is about what happened to the performance of Portuguese public hospitals. The main goal of this work was to test if the Portuguese public hospitals’ performance has been affected by the SARS-CoV-2 pandemic. We used the Benefit-of-Doubt method integrated with the Malmquist Index to analyze the performance evolution over time. Then, we employed a multiple regression model to test whether some pandemic-related variables could explain the performance results. We considered a database of 40 Portuguese public hospitals evaluated from January 2017 to May 2022. The period 2017 to 2019 corresponds to the baseline (pre-pandemic), against which the remaining period will be compared (during the pandemic). We also considered fourteen variables characterizing hospital quality, divided into three main performance definitions (efficiency and productivity; access; safety and care appropriateness). As potential explanatory variables, we consider seven dimensions, including vaccination rate and the need for intensive care for COVID-19-infected people. The results suggest that COVID-19 pandemic features help explain the drop in access after 2020, but not the evolution of safety and appropriateness of care, which surprisingly increased the whole time.

Mutations of SARS-CoV-2 Structural Proteins in the Alpha, Beta, Gamma, and Delta Variants: Bioinformatics Analysis

Background

COVID-19 and Middle East Respiratory Syndrome are two pandemic respiratory diseases caused by coronavirus species. The novel disease COVID-19 caused by SARS-CoV-2 was first reported in Wuhan, Hubei Province, China, in December 2019, and became a pandemic within 2-3 months, affecting social and economic platforms worldwide. Despite the rapid development of vaccines, there have been obstacles to their distribution, including a lack of fundamental resources, poor immunization, and manual vaccine replication. Several variants of the original Wuhan strain have emerged in the last 3 years, which can pose a further challenge for control and vaccine development.

Objective

The aim of this study was to comprehensively analyze mutations in SARS-CoV-2 variants of concern (VoCs) using a bioinformatics approach toward identifying novel mutations that may be helpful in developing new vaccines by targeting these sites.

Methods

Reference sequences of the SARS-CoV-2 spike (YP_009724390) and nucleocapsid (YP_009724397) proteins were compared to retrieved sequences of isolates of four VoCs from 14 countries for mutational and evolutionary analyses. Multiple sequence alignment was performed and phylogenetic trees were constructed by the neighbor-joining method with 1000 bootstrap replicates using MEGA (version 6). Mutations in amino acid sequences were analyzed using the MultAlin online tool (version 5.4.1).

Results

Among the four VoCs, a total of 143 nonsynonymous mutations and 8 deletions were identified in the spike and nucleocapsid proteins. Multiple sequence alignment and amino acid substitution analysis revealed new mutations, including G72W, M2101I, L139F, 209-211 deletion, G212S, P199L, P67S, I292T, and substitutions with unknown amino acid replacement, reported in Egypt (MW533289), the United Kingdom (MT906649), and other regions. The variants B.1.1.7 (Alpha variant) and B.1.617.2 (Delta variant), characterized by higher transmissibility and lethality, harbored the amino acid substitutions D614G, R203K, and G204R with higher prevalence rates in most sequences. Phylogenetic analysis among the novel SARS-CoV-2 variant proteins and some previously reported β-coronavirus proteins indicated that either the evolutionary clade was weakly supported or not supported at all by the β-coronavirus species.

Conclusions

This study could contribute toward gaining a better understanding of the basic nature of SARS-CoV-2 and its four major variants. The numerous novel mutations detected could also provide a better understanding of VoCs and help in identifying suitable mutations for vaccine targets. Moreover, these data offer evidence for new types of mutations in VoCs, which will provide insight into the epidemiology of SARS-CoV-2.

Spotlight on contributory role of host immunogenetic profiling in SARS-CoV-2 infection: Susceptibility, severity, mortality, and vaccine effectiveness

BACKGROUND

The SARS-CoV-2 virus has spread continuously worldwide, characterized by various clinical symptoms. The immune system responds to SARS-CoV-2 infection by producing Abs and secreting cytokines. Recently, numerous studies have highlighted that immunogenetic factors perform a putative role in COVID-19 pathogenesis and implicate vaccination effectiveness.

AIM

This review summarizes the relevant articles and evaluates the significance of mutation and polymorphism in immune-related genes regarding susceptibility, severity, mortality, and vaccination effectiveness of COVID-19. Furthermore, the correlation between host immunogenetic and SARS-CoV-2 reinfection is discussed.

METHOD

A comprehensive search was conducted to identify relevant articles using five databases until January 2023, which resulted in 105 total articles.

KEY FINDINGS

Taken to gather this review summarized that: (a) there is a plausible correlation between immune-related genes and COVID-19 outcomes, (b) the HLAs, cytokines, chemokines, and other immune-related genes expression profiles can be a prognostic factor in COVID-19-infected patients, and (c) polymorphisms in immune-related genes have been associated with the effectiveness of vaccination.

SIGNIFICANCE

Regarding the importance of mutation and polymorphisms in immune-related genes in COVID-19 outcomes, modulating candidate genes is expected to help clinical decisions, patient outcomes management, and innovative therapeutic approach development. In addition, the manipulation of host immunogenetics is hypothesized to induce more robust cellular and humoral immune responses, effectively increase the efficacy of vaccines, and subsequently reduce the incidence rates of reinfection-associated COVID-19.

Coronary microvascular dysfunction and cardiovascular disease: Pathogenesis, associations and treatment strategies

Coronary microvascular dysfunction (CMD) is a high-risk factor for a variety of cardiovascular events. Due to its complex aetiology and concealability, knowledge of the pathophysiological mechanism of CMD is still limited at present, which greatly restricts its clinical diagnosis and treatment. Studies have shown that CMD is closely related to a variety of cardiovascular diseases, can aggravate the occurrence and development of cardiovascular diseases, and is closely related to a poor prognosis in patients with cardiovascular diseases. Improving coronary microvascular remodelling and increasing myocardial perfusion might be promising strategies for the treatment of cardiovascular diseases. In this paper, the pathogenesis and functional assessment of CMD are reviewed first, along with the relationship of CMD with cardiovascular diseases. Then, the latest strategies for the treatment of CMD and cardiovascular diseases are summarized. Finally, urgent scientific problems in CMD and cardiovascular diseases are highlighted and future research directions are proposed to provide prospective insights for the prevention and treatment of CMD and cardiovascular diseases in the future.

Gender Differences in Response to COVID-19 Infection and Vaccination

Since COVID-19 first appeared, a number of follow-up events have taken place. In an effort to find a solution to this catastrophe, a great deal of study and analysis has been conducted. Because of the high morbidity and exceptionally large losses, scientists are being pushed to conduct more research and find vaccination and treatments. The virus has a wide range of effects, one of which is how it affects sexual activity in both men and women. The impact of the cardiovascular system and susceptibility to embolism, lung stress, and infection heightens the probability of hospitalization in the intensive care unit for pregnant women who have contracted COVID-19. There is no evidence of infection being passed from mother to child. In the current review, the role of COVID-19 infection and vaccination on male and female sexual activity, hormones, and the menstrual cycle for females, as well as on male sex hormones and sexual activity during infection and after vaccination, are being investigated. There are no reports of the virus being isolated from the semen of an infected patient or recently recovered patients. A recent investigation on the influence of the virus on gender susceptibility to sexual organs and function has been uncovered throughout this study.

Role of E3 ubiquitin ligases and deubiquitinating enzymes in SARS-CoV-2 infection

Ever since its emergence in 2019, COVID-19 has rapidly disseminated worldwide, engendering a pervasive pandemic that has profoundly impacted healthcare systems and the socio-economic milieu. A plethora of studies has been conducted targeting its pathogenic virus, SARS-CoV-2, to find ways to combat COVID-19. The ubiquitin-proteasome system (UPS) is widely recognized as a crucial mechanism that regulates human biological activities by maintaining protein homeostasis. Within the UPS, the ubiquitination and deubiquitination, two reversible modifications, of substrate proteins have been extensively studied and implicated in the pathogenesis of SARS-CoV-2. The regulation of E3 ubiquitin ligases and DUBs(Deubiquitinating enzymes), which are key enzymes involved in the two modification processes, determines the fate of substrate proteins. Proteins associated with the pathogenesis of SARS-CoV-2 may be retained, degraded, or even activated, thus affecting the ultimate outcome of the confrontation between SARS-CoV-2 and the host. In other words, the clash between SARS-CoV-2 and the host can be viewed as a battle for dominance over E3 ubiquitin ligases and DUBs, from the standpoint of ubiquitin modification regulation. This review primarily aims to clarify the mechanisms by which the virus utilizes host E3 ubiquitin ligases and DUBs, along with its own viral proteins that have similar enzyme activities, to facilitate invasion, replication, escape, and inflammation. We believe that gaining a better understanding of the role of E3 ubiquitin ligases and DUBs in COVID-19 can offer novel and valuable insights for developing antiviral therapies.

Novel Mode of nanoLuciferase Packaging in SARS-CoV-2 Virions and VLPs Provides Versatile Reporters for Virus Production

SARS-CoV-2 is a positive-strand RNA virus in the Coronaviridae family that is responsible for morbidity and mortality worldwide. To better understand the molecular pathways leading to SARS-CoV-2 virus assembly, we examined a virus-like particle (VLP) system co-expressing all structural proteins together with an mRNA reporter encoding nanoLuciferase (herein nLuc). Surprisingly, the 19 kDa nLuc protein itself was encapsidated into VLPs, providing a better reporter than nLuc mRNA itself. Strikingly, infecting nLuc-expressing cells with the SARS-CoV-2, NL63 or OC43 coronaviruses yielded virions containing packaged nLuc that served to report viral production. In contrast, infection with the flaviviruses, dengue or Zika, did not lead to nLuc packaging and secretion. A panel of reporter protein variants revealed that the packaging is size-limited and requires cytoplasmic expression, indicating that the large virion of coronaviruses can encaspidate a small cytoplasmic reporter protein. Our findings open the way for powerful new approaches to measure coronavirus particle production, egress and viral entry mechanisms.

Repurposing clinically available drugs and therapies for pathogenic targets to combat SARS-CoV-2

The coronavirus disease 2019 (COVID-19) pandemic has affected a large portion of the global population, both physically and mentally. Current evidence suggests that the rapidly evolving coronavirus subvariants risk rendering vaccines and antibodies ineffective due to their potential to evade existing immunity, with enhanced transmission activity and higher reinfection rates that could lead to new outbreaks across the globe. The goal of viral management is to disrupt the viral life cycle as well as to relieve severe symptoms such as lung damage, cytokine storm, and organ failure. In the fight against viruses, the combination of viral genome sequencing, elucidation of the structure of viral proteins, and identifying proteins that are highly conserved across multiple coronaviruses has revealed many potential molecular targets. In addition, the time- and cost-effective repurposing of preexisting antiviral drugs or approved/clinical drugs for these targets offers considerable clinical advantages for COVID-19 patients. This review provides a comprehensive overview of various identified pathogenic targets and pathways as well as corresponding repurposed approved/clinical drugs and their potential against COVID-19. These findings provide new insight into the discovery of novel therapeutic strategies that could be applied to the control of disease symptoms emanating from evolving SARS-CoV-2 variants.

Pharmaceutical approaches for COVID-19: An update on current therapeutic opportunities

SARS-CoV-2, a newly discovered coronavirus, has been linked to the COVID-19 pandemic and is currently an important public health issue. Despite all the work done to date around the world, there is still no viable treatment for COVID-19. This study examined the most recent evidence on the efficacy and safety of several therapeutic options available including natural substances, synthetic drugs and vaccines in the treatment of COVID-19. Various natural compounds such as sarsapogenin, lycorine, biscoclaurine, vitamin B₁₂, glycyrrhizic acid, riboflavin, resveratrol and kaempferol, various vaccines and drugs such as AZD1222, mRNA-1273, BNT162b2, Sputnik V, and remdesivir, lopinavir, favipiravir, darunavir, oseltamivir, and umifenovir, resp., have been discussed comprehensively. We attempted to provide exhaustive information regarding the various prospective therapeutic approaches available in order to assist researchers and physicians in treating COVID-19 patients.

PI3K/Akt/Nrf2 mediated cellular signaling and virus-host interactions: latest updates on the potential therapeutic management of SARS-CoV-2 infection

The emergence and re-emergence of viral diseases, which cause significant global mortality and morbidity, are the major concerns of this decade. Of these, current research is focused majorly on the etiological agent of the COVID-19 pandemic, SARS-CoV-2. Understanding the host response and metabolic changes during viral infection may provide better therapeutic targets for the proper management of pathophysiological conditions associated with SARS-CoV-2 infection. We have achieved control over most emerging viral diseases; however, a lack of understanding of the underlying molecular events prevents us from exploring novel therapeutic targets, leaving us forced to witness re-emerging viral infections. SARS-CoV-2 infection is usually accompanied by oxidative stress, which leads to an overactive immune response, the release of inflammatory cytokines, increasing lipid production, and also alterations in the endothelial and mitochondrial functions. PI3K/Akt signaling pathway confers protection against oxidative injury by various cell survival mechanisms including Nrf2-ARE mediated antioxidant transcriptional response. SARS-CoV-2 is also reported to hijack this pathway for its survival within host and few studies have suggested the role of antioxidants in modulating the Nrf2 pathway to manage disease severity. This review highlights the interrelated pathophysiological conditions associated with SARS-CoV-2 infection and the host survival mechanisms mediated by PI3K/Akt/Nrf2 signaling pathways that can help ameliorate the severity of the disease and provide effective antiviral targets against SARS-CoV-2.

Monomeric and dimeric states of human ZO1-PDZ2 are functional partners of the SARS-CoV-2 E protein

The Envelope (E) protein of SARS-CoV-2 plays a key role in virus maturation, assembly, and virulence mechanisms. The E protein is characterized by the presence of a PDZ-binding motif (PBM) at its C-terminus that allows it to interact with several PDZ-containing proteins in the intracellular environment. One of the main binding partners of the SARS-CoV-2 E protein is the PDZ2 domain of ZO1, a protein with a crucial role in the formation of epithelial and endothelial tight junctions (TJs). In this work, through a combination of analytical ultracentrifugation analysis and equilibrium and kinetic folding experiments, we show that ZO1-PDZ2 domain is able to fold in a monomeric state, an alternative form to the dimeric conformation that is reported to be functional in the cell for TJs assembly. Importantly, surface plasmon resonance (SPR) data indicate that the PDZ2 monomer is fully functional and capable of binding the C-terminal portion of the E protein of SARS-CoV-2, with a measured affinity in the micromolar range. Moreover, we present a detailed computational analysis of the complex between the C-terminal portion of E protein with ZO1-PDZ2, both in its monomeric conformation (computed as a high confidence AlphaFold2 model) and dimeric conformation (obtained from the Protein Data Bank), by using both polarizable and nonpolarizable simulations. Together, our results indicate both the monomeric and dimeric states of PDZ2 to be functional partners of the E protein, with similar binding mechanisms, and provide mechanistic and structural information about a fundamental interaction required for the replication of SARS-CoV-2.

Different electrostatic forces drive the binding kinetics of SARS-CoV, SARS-CoV-2 and MERS-CoV Envelope proteins with the PDZ2 domain of ZO1

The Envelope protein (E) is a structural protein encoded by the genome of SARS-CoV, SARS-CoV-2 and MERS-CoV Coronaviruses. It is poorly present in the virus but highly expressed in the host cell, with prominent role in virus assembly and virulence. The E protein possesses a PDZ-binding motif (PBM) at its C terminus that allows it to interact with host PDZ domain containing proteins. ZO1 is a key protein in assembling the cytoplasmic plaque of epithelial and endothelial Tight Junctions (TJs) as well as in determining cell differentiation, proliferation and polarity. The PDZ2 domain of ZO1 is known to interact with the Coronaviruses Envelope proteins, however the molecular details of such interaction have not been established. In this paper we directly measured, through Fluorescence Resonance Energy Transfer and Stopped-Flow methodology, the binding kinetics of the PDZ2 domain of ZO1 with peptides mimicking the C-terminal portion of the Envelope protein from SARS-CoV, SARS-CoV-2 and MERS-CoV in different ionic strength conditions. Interestingly, the peptide mimicking the E protein from MERS-CoV display much higher microscopic association rate constant with PDZ2 compared to SARS-CoV and SARS-CoV-2 suggesting a stronger contribution of electrostatic forces in the early events of binding. A comparison of thermodynamic and kinetic data obtained at increasing ionic strengths put in evidence different contribution of electrostatics in the recognition and complex formation events for the three peptides. Our data are discussed under the light of available structural data of PDZ2 domain of ZO1 and of previous works about these protein systems.

Structural and non-structural proteins in SARS-CoV-2: potential aspects to COVID-19 treatment or prevention of progression of related diseases

Coronavirus disease 2019 (COVID-19) is caused by a new member of the Coronaviridae family known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). There are structural and non-structural proteins (NSPs) in the genome of this virus. S, M, H, and E proteins are structural proteins, and NSPs include accessory and replicase proteins. The structural and NSP components of SARS-CoV-2 play an important role in its infectivity, and some of them may be important in the pathogenesis of chronic diseases, including cancer, coagulation disorders, neurodegenerative disorders, and cardiovascular diseases. The SARS-CoV-2 proteins interact with targets such as angiotensin-converting enzyme 2 (ACE2) receptor. In addition, SARS-CoV-2 can stimulate pathological intracellular signaling pathways by triggering transcription factor hypoxia-inducible factor-1 (HIF-1), neuropilin-1 (NRP-1), CD147, and Eph receptors, which play important roles in the progression of neurodegenerative diseases like Alzheimer's disease, epilepsy, and multiple sclerosis, and multiple cancers such as glioblastoma, lung malignancies, and leukemias. Several compounds such as polyphenols, doxazosin, baricitinib, and ruxolitinib could inhibit these interactions. It has been demonstrated that the SARS-CoV-2 spike protein has a stronger affinity for human ACE2 than the spike protein of SARS-CoV, leading the current study to hypothesize that the newly produced variant Omicron receptor-binding domain (RBD) binds to human ACE2 more strongly than the primary strain. SARS and Middle East respiratory syndrome (MERS) viruses against structural and NSPs have become resistant to previous vaccines. Therefore, the review of recent studies and the performance of current vaccines and their effects on COVID-19 and related diseases has become a vital need to deal with the current conditions. This review examines the potential role of these SARS-CoV-2 proteins in the initiation of chronic diseases, and it is anticipated that these proteins could serve as components of an effective vaccine or treatment for COVID-19 and related diseases. Video Abstract.

pH-dependent endocytosis mechanisms for influenza A and SARS-coronavirus

The ongoing SARS-CoV-2 pandemic and the influenza epidemics have revived the interest in understanding how these highly contagious enveloped viruses respond to alterations in the physicochemical properties of their microenvironment. By understanding the mechanisms and conditions by which viruses exploit the pH environment of the host cell during endocytosis, we can gain a better understanding of how they respond to pH-regulated anti-viral therapies but also pH-induced changes in extracellular environments. This review provides a detailed explanation of the pH-dependent viral structural changes preceding and initiating viral disassembly during endocytosis for influenza A (IAV) and SARS coronaviruses. Drawing upon extensive literature from the last few decades and latest research, I analyze and compare the circumstances in which IAV and SARS-coronavirus can undertake endocytotic pathways that are pH-dependent. While there are similarities in the pH-regulated patterns leading to fusion, the mechanisms and pH activation differ. In terms of fusion activity, the measured activation pH values for IAV, across all subtypes and species, vary between approximately 5.0 to 6.0, while SARS-coronavirus necessitates a lower pH of 6.0 or less. The main difference between the pH-dependent endocytic pathways is that the SARS-coronavirus, unlike IAV, require the presence of specific pH-sensitive enzymes (cathepsin L) during endosomal transport. Conversely, the conformational changes in the IAV virus under acidic conditions in endosomes occur due to the specific envelope glycoprotein residues and envelope protein ion channels (viroporins) getting protonated by H+ ions. Despite extensive research over several decades, comprehending the pH-triggered conformational alterations of viruses still poses a significant challenge. The precise mechanisms of protonation mechanisms of certain during endosomal transport for both viruses remain incompletely understood. In absence of evidence, further research is needed.

SARS-CoV-2 envelope protein triggers depression-like behaviors and dysosmia via TLR2-mediated neuroinflammation in mice

BACKGROUND

Depression and dysosmia have been regarded as primary neurological symptoms in COVID-19 patients, the mechanism of which remains unclear. Current studies have demonstrated that the SARS-CoV-2 envelope (E) protein is a pro-inflammatory factor sensed by Toll-like receptor 2 (TLR2), suggesting the pathological feature of E protein is independent of viral infection. In this study, we aim to ascertain the role of E protein in depression, dysosmia and associated neuroinflammation in the central nervous system (CNS).

METHODS

Depression-like behaviors and olfactory function were observed in both female and male mice receiving intracisternal injection of E protein. Immunohistochemistry was applied in conjunction with RT-PCR to evaluate glial activation, blood-brain barrier status and mediators synthesis in the cortex, hippocampus and olfactory bulb. TLR2 was pharmacologically blocked to determine its role in E protein-related depression-like behaviors and dysosmia in mice.

RESULTS

Intracisternal injection of E protein evoked depression-like behaviors and dysosmia in both female and male mice. Immunohistochemistry suggested that the E protein upregulated IBA1 and GFAP in the cortex, hippocampus and olfactory bulb, while ZO-1 was downregulated. Moreover, IL-1β, TNF-α, IL-6, CCL2, MMP2 and CSF1 were upregulated in both cortex and hippocampus, whereas IL-1β, IL-6 and CCL2 were upregulated in the olfactory bulb. Furtherly, inhibiting microglia, rather than astrocytes, alleviated depression-like behaviors and dysosmia induced by E protein. Finally, RT-PCR and immunohistochemistry suggested that TLR2 was upregulated in the cortex, hippocampus and olfactory bulb, the blocking of which mitigated depression-like behaviors and dysosmia induced by E protein.

CONCLUSIONS

Our study demonstrates that envelope protein could directly induce depression-like behaviors, dysosmia, and obvious neuroinflammation in CNS. TLR2 mediated depression-like behaviors and dysosmia induced by envelope protein, which could serve as a promising therapeutic target for neurological manifestation in COVID-19 patients.

One stone two birds: anti-inflammatory bronchodilators as a potential pharmacological strategy for COVID-19

The ongoing Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has imposed a huge threat to public health across the world. While vaccinations are essential for reducing virus transmission and attenuating disease severity, the nature of high mutation rate of SARS-CoV-2 renders vaccines less effective, urging quick development of effective therapies for COVID-19 disease. However, developing novel drugs remains extremely challenging due to the lengthy process and high cost. Alternatively, repurposing of existing drugs on the market represents a rapid and safe strategy for combating COVID-19 pandemic. Bronchodilators are first line drugs for inflammatory lung diseases, such as asthma and chronic obstructive pulmonary disease (COPD). Compared to other anti-inflammatory drugs repurposed for COVID-19, bronchodilators are unique in that they have both anti-inflammatory and bronchodilating properties. Whether the dual properties of bronchodilators empower them greater potential to be repurposed for COVID-19 is worth exploring. In fact, clinical and preclinical studies have recently emerged to investigate the benefits of bronchodilators such assalbutamol, formoterol and theophylline in treating COVID-19, and many of them have shown encouraging efficacy on attenuating disease severity of pneumonia and other associated symptoms. To comprehensively understand the latest progress on COVID-19 intervention with bronchodilators, this review will summarize recent findings in this area and highlight the promising clinical benefits and possible adverse effects of bronchodilators as therapeutic options for COVID-19 with a focus on β2 receptor agonists, anticholinergic drugs and theophylline.

Perturbation of the host cell Ca2+ homeostasis and ER-mitochondria contact sites by the SARS-CoV-2 structural proteins E and M

Coronavirus disease (COVID-19) is a contagious respiratory disease caused by the SARS-CoV-2 virus. The clinical phenotypes are variable, ranging from spontaneous recovery to serious illness and death. On March 2020, a global COVID-19 pandemic was declared by the World Health Organization (WHO). As of February 2023, almost 670 million cases and 6,8 million deaths have been confirmed worldwide. Coronaviruses, including SARS-CoV-2, contain a single-stranded RNA genome enclosed in a viral capsid consisting of four structural proteins: the nucleocapsid (N) protein, in the ribonucleoprotein core, the spike (S) protein, the envelope (E) protein, and the membrane (M) protein, embedded in the surface envelope. In particular, the E protein is a poorly characterized viroporin with high identity amongst all the β-coronaviruses (SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-OC43) and a low mutation rate. Here, we focused our attention on the study of SARS-CoV-2 E and M proteins, and we found a general perturbation of the host cell calcium (Ca2+) homeostasis and a selective rearrangement of the interorganelle contact sites. In vitro and in vivo biochemical analyses revealed that the binding of specific nanobodies to soluble regions of SARS-CoV-2 E protein reversed the observed phenotypes, suggesting that the E protein might be an important therapeutic candidate not only for vaccine development, but also for the clinical management of COVID designing drug regimens that, so far, are very limited.

A Candidate Antigen of the Recombinant Membrane Protein Derived from the Porcine Deltacoronavirus Synthetic Gene to Detect Seropositive Pigs

Porcine deltacoronavirus (PDCoV) is an emergent swine coronavirus which infects cells from the small intestine and induces watery diarrhea, vomiting and dehydration, causing mortality in piglets (>40%). The aim of this study was to evaluate the antigenicity and immunogenicity of the recombinant membrane protein (M) of PDCoV (rM-PDCoV), which was developed from a synthetic gene obtained after an in silico analysis with a group of 138 GenBank sequences. A 3D model and phylogenetic analysis confirmed the highly conserved M protein structure. Therefore, the synthetic gene was successfully cloned in a pETSUMO vector and transformed in E. coli BL21 (DE3). The rM-PDCoV was confirmed by SDS-PAGE and Western blot with ~37.7 kDa. The rM-PDCoV immunogenicity was evaluated in immunized (BLAB/c) mice and iELISA. The data showed increased antibodies from 7 days until 28 days (p < 0.001). The rM-PDCoV antigenicity was analyzed using pig sera samples from three states located in "El Bajío" Mexico and positive sera were determined. Our results show that PDCoV has continued circulating on pig farms in Mexico since the first report in 2019; therefore, the impact of PDCoV on the swine industry could be higher than reported in other studies.

Stability of SARS-CoV-2 on inanimate surfaces: A review

The stability of SARS-CoV-2 for varying periods on a wide range of inanimate surfaces has raised concerns about surface transmission; however, there is still no evidence to confirm this route. In the present review, three variables affecting virus stability, namely temperature, relative humidity (RH), and initial virus titer, were considered from different experimental studies. The stability of SARS-CoV-2 on the surfaces of six different contact materials, namely plastic, metal, glass, protective equipment, paper, and fabric, and the factors affecting half-life period was systematically reviewed. The results showed that the half-life of SARS-CoV-2 on different contact materials was generally 2-10 h, up to 5 d, and as short as 30 min at 22 °C, whereas the half-life of SARS-CoV-2 on non-porous surfaces was generally 5-9 h d, up to 3 d, and as short as 4 min at 22 ℃. The half-life on porous surfaces was generally 1-5 h, up to 2 d, and as short as 13 min at 22 °C. Therefore, the half-life period of SARS-CoV-2 on non-porous surfaces is longer than that on porous surfaces, and thehalf-life of the virus decreases with increasing temperature, whereas RH produces a stable negative inhibitory effect only in a specific humidity range. Various disinfection precautions can be implemented in daily life depending on the stability of SARS-CoV-2 on different surfaces to interrupt virus transmission, prevent COVID-19 infections, and avoid over-disinfection. Owing to the more stringent control of conditions in laboratory studies and the lack of evidence of transmission through surfaces in the real world, it is difficult to provide strong evidence for the efficiency of transmission of the contaminant from the surface to the human body. Therefore, we suggest that future research should focus on exploring the systematic study of the entire transmission process of the virus, which will provide a theoretical basis for optimizing global outbreak prevention and control measures.

The Envelope (E) Protein of SARS-CoV-2 as a Pharmacological Target

The COVID-19 pandemic caused by the SARS-CoV-2 virus is still a global health concern. Several spike (S) protein-based vaccines have been developed that efficiently protect the human population against severe forms of COVID-19. However, some SARS-CoV-2 variants of concern (VOCs) have emerged that evade the protective effect of vaccine-induced antibodies. Therefore, efficient and specific antiviral treatments to control COVID-19 are indispensable. To date, two drugs have been approved for mild COVID-19 treatment; nevertheless, more drugs, preferably broad-spectrum and ready-to-use therapeutic agents for new pandemics, are needed. Here, I discuss the PDZ-dependent protein-protein interactions of the viral E protein with host proteins as attractive alternatives for the development of antivirals against coronavirus.

Insight into the liver dysfunction in COVID-19 patients: Molecular mechanisms and possible therapeutic strategies

As of June 2022, more than 530 million people worldwide have become ill with coronavirus disease 2019 (COVID-19). Although COVID-19 is most commonly associated with respiratory distress (severe acute respiratory syndrome), meta-analysis have indicated that liver dysfunction also occurs in patients with severe symptoms. Current studies revealed distinctive patterning in the receptors on the hepatic cells that helps in viral invasion through the expression of angiotensin-converting enzyme receptors. It has also been reported that in some patients with COVID-19, therapeutic strategies, including repurposed drugs (mitifovir, lopinavir/ritonavir, tocilizumab, etc.) triggered liver injury and cholestatic toxicity. Several proven indicators support cytokine storm-induced hepatic damage. Because there are 1.5 billion patients with chronic liver disease worldwide, it becomes imperative to critically evaluate the molecular mechanisms concerning hepatotropism of COVID-19 and identify new potential therapeutics. This review also designated a comprehensive outlook of comorbidities and the impact of lifestyle and genetics in managing patients with COVID-19.

Exploring polyamine interactions and binding pockets in SARS-CoV-2 ORF3a

Ongoing global pandemic caused by coronavirus (COVID-19) requires urgent development of vaccines, treatments, and diagnostic tools. Open reading frame 3a (ORF3a) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is considered to be a potential drug target for COVID-19 treatment. ORF3a is an accessory protein that plays a significant role in virus-host interactions and in facilitating host immune responses. Using putrescine, spermidine and spermine, an aliphatic polyamine for the activity suppression of ORF3a appears to be a promising approach in finding new targets for drug design. In this study, we explored the possible binding poses of polyamines to the ORF3a protein using a combination of various computational approaches i.e. pocket prediction, blind and site-specific molecular docking, molecular dynamics and ligand flooding simulations. The results showed that the tip of cytoplasmic domain and the upper tunnel of transmembrane domain of ORF3a provide a suitable binding site specific for the polyamines. MD simulations revealed the stability of spermidine binding in the upper tunnel pocket of ORF3a through salt bridge and hydrogen bond interactions between the amine groups of the ligand and negatively charged residues of ORF3a. These findings can be helpful in designing new therapeutic drugs.