SARS-CoV, MERS-CoV, and 2019-nCoV viruses: an overview of origin, evolution, and genetic variations

Impact of mutations in immunodominant regions of SARS-CoV-2 variants on recognition by CD8+ T cell: An in silico analysis

BACKGROUND

This study aimed to investigate whether mutations in the immunodominant regions of the S, M, and N proteins of the Gamma, Delta, and Omicron SARS-CoV-2 variants that circulated in Brazil affect the recognition of viral antigens by Brazilian HLA-I-restricted CD8+ T cell epitopes, using an in silico approach.

METHODS

Sequences of the Gamma (n = 36,174), Delta (n = 35,129), and Omicron (n = 336) variants were retrieved using GISAID. Consensus sequences were generated using Geneious software with NC045512 as a reference. Epitopes for the S, M, and N proteins of both the original and variant sequences were predicted using NetCTLpan 1.1, NetMHCpan 4.0, and VaxiJen v2.0. The positions occupied by these epitopes, with high probability of presentation, affinity to HLA molecules, and antigenicity, were identified as potentially immunodominant regions.

RESULTS

The S protein of the reference sequence (NC045512) and its variants contained 17 immunodominant regions. Delta showed the highest conservation (94.1 %, 16), followed by Gamma (82.3 %, 14) and Omicron (70.5 %, 12). Omicron exhibited the greatest mutational variability and had regions of increased antigenicity and two novel immunodominant regions with broader human leukocyte antigen (HLA) recognition. Additionally, Omicron lost two previously identified immunodominant regions and had one region of reduced antigenicity that did not affect HLA recognition. Gamma had mutations in three regions that increased both antigenicity and HLA recognition. Delta had only one mutated region with lower antigenicity, which did not affect HLA recognition. Notably, new immunodominant regions for the M and N proteins appeared in the Omicron variant.

CONCLUSIONS

Brazilian HLA-I-restricted CD8+ T cell epitopes from SARS-CoV-2 immunodominant regions are partially conserved in the Gamma, Delta, and Omicron variants circulating in Brazil, suggesting effective a cross-protective immune response that may help reduce COVID-19 severity and mortality.

Thousands-years-old deep-sea DNA viruses reveal the evolution of human pathogenic viruses

INTRODUCTION

In the last two decades, outbreaks of pathogenic viruses have led to significant human mortality and economic repercussions. Despite extensive investigations into tracing these viruses in terrestrial environments, their origins remain enigmatic.

OBJECTIVES

The Earth's biosphere encompasses both sunlight-dependent terrestrial and surface ocean ecosystems, as well as the sunlight-independent deep-sea ecosystem. However, the traceability of human pathogenic viruses in the deep sea has not been thoroughly explored. This study aimed to investigate the presence of human pathogenic viruses in the deep sea.

METHODS

In this study, we performed a viral metagenomic analysis using a global deep-sea sediment virome 2.0 dataset which contained 159 deep-sea sediment samples with geologic ages from 2,500 to 7,750 years.

RESULTS

A total of 554,664 viral operational taxonomic units (vOTUs) were identified and further obtained 2,254 potential pathogenic viruses of vertebrates. Among them, 23 vOTUs exhibited high homology with 12 species of human pathogenic viruses which belonged to 4 viral families. Notably, variola virus, the first human pathogenic virus eradicated from humans and now only found in laboratories, was discovered in the ancient deep-sea sediments. The evolution analysis showed that these DNA viruses might represent the ancestors or variants of human pathogenic viruses, suggesting that the deep sea could be a crucial reservoir for human pathogenic viruses.

CONCLUSION

Our findings present all the ancient pathogenic DNA viruses of humans found in the deep sea for the first time, highlighting the source of the future epidemics. It is imperative to implement the stringent virus monitoring and management measures for human activities in marine environments to address the emerging challenges of marine biosecurity and promote sustainable use of oceans.

Viral N protein hijacks deaminase-containing RNA granules to enhance SARS-CoV-2 mutagenesis

Host cell-encoded deaminases act as antiviral restriction factors to impair viral replication and production through introducing mutations in the viral genome. We sought to understand whether deaminases are involved in SARS-CoV-2 mutation and replication, and how the viral factors interact with deaminases to trigger these processes. Here, we show that APOBEC and ADAR deaminases act as the driving forces for SARS-CoV-2 mutagenesis, thereby blocking viral infection and production. Mechanistically, SARS-CoV-2 nucleocapsid (N) protein, which is responsible for packaging viral genomic RNA, interacts with host deaminases and co-localizes with them at stress granules to facilitate viral RNA mutagenesis. N proteins from several coronaviruses interact with host deaminases at RNA granules in a manner dependent on its F17 residue, suggesting a conserved role in modulation of viral mutagenesis in other coronaviruses. Furthermore, mutant N protein bearing a F17A substitution cannot localize to deaminase-containing RNA granules and leads to reduced mutagenesis of viral RNA, providing support for its function in enhancing deaminase-dependent viral RNA editing. Our study thus provides further insight into virus-host cell interactions mediating SARS-CoV-2 evolution.

Affinity Tag-Free Purification of SARS-CoV-2 N Protein and Its Crystal Structure in Complex with ssDNA

The nucleocapsid (N) protein is one of the four structural proteins in SARS-CoV-2, playing key roles in viral assembly, immune evasion, and stability. One of its primary functions is to protect viral RNA by forming the nucleocapsid. However, the precise mechanisms by which the N protein interacts with viral RNA and assembles into a nucleocapsid remain unclear. Compared to other SARS-CoV-2 components, targeting the N protein has several advantages: it exhibits higher sequence conservation, lower mutation rates, and stronger immunogenicity, making it an attractive target for antiviral drug development and diagnostics. Therefore, a detailed understanding of the N protein's structure is essential for deciphering its role in viral assembly and developing effective therapeutics. In this study, we report the expression and purification of a soluble recombinant N protein, along with a 1.55 Å resolution crystal structure of its nucleic acid-binding domain (N-NTD) in complex with ssDNA. Our structure revealed new insights into the conformation and interaction of the flexible N-arm, which could aid in understanding nucleocapsid assembly. Additionally, we identified residues that are critical for ssDNA interaction.

In Silico Identification of Potential Inhibitors of SARS-CoV-2 Main Protease (Mpro)

The ongoing Coronavirus Disease 19 (COVID-19) pandemic has had a profound impact on the global healthcare system. As the SARS-CoV-2 virus, responsible for this pandemic, continues to spread and develop mutations in its genetic material, new variants of interest (VOIs) and variants of concern (VOCs) are emerging. These outbreaks lead to a decrease in the efficacy of existing treatments such as vaccines or drugs, highlighting the urgency of new therapies for COVID-19. Therefore, in this study, we aimed to identify potential SARS-CoV-2 antivirals using a virtual screening protocol and molecular dynamics simulations. These techniques allowed us to predict the binding affinity of a database of compounds with the virus Mpro protein. This in silico approach enabled us to identify twenty-two chemical structures from a public database (QSAR Toolbox Ver 4.5 ) and ten promising molecules from our in-house database. The latter molecules possess advantageous qualities, such as two-step synthesis, cost-effectiveness, and long-lasting physical and chemical stability. Consequently, these molecules can be considered as promising alternatives to combat emerging SARS-CoV-2 variants.

A mathematical model of mobility-related infection and vaccination in an epidemiological case

In this study, we established a system of differential equations with piecewise constant arguments to explain the impact of epidemiological transmission between different locations. Our main goal is to look into the need for vaccines as well as the necessity of the lockdown period. We proved that keeping social distance was necessary during the pandemic spread to stop transmissions between different locations and that re-vaccinations, including screening tests, were crucial to avoid reinfections. Using the Routh-Hurwitz Criterion, we examined the model's local stability and demonstrated that the system could experience Stationary and Neimark-Sacker bifurcations depending on certain circumstances.

Sulfated Glycans Inhibit the Interaction of MERS-CoV Receptor Binding Domain with Heparin

Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic virus with high contagion and mortality rates. Heparan sulfate proteoglycans (HSPGs) are ubiquitously expressed on the surface of mammalian cells. Owing to its high negatively charged property, heparan sulfate (HS) on the surface of host cells is used by many viruses as cofactor to facilitate viral attachment and initiate cellular entry. Therefore, inhibition of the interaction between viruses and HS could be a promising target to inhibit viral infection. In the current study, the interaction between the receptor-binding domain (RBD) of MERS-CoV and heparin was exploited to assess the inhibitory activity of various sulfated glycans such as glycosaminoglycans, marine-sourced glycans (sulfated fucans, fucosylated chondroitin sulfates, fucoidans, and rhamnan sulfate), pentosan polysulfate, and mucopolysaccharide using Surface Plasmon Resonance. We believe this study provides valuable insights for the development of sulfated glycan-based inhibitors as potential antiviral agents.

SARS-CoV-2 and Brain Health: New Challenges in the Era of the Pandemic

Respiratory viral infections have been found to have a negative impact on neurological functions, potentially leading to significant neurological impairment. The SARS-CoV-2 virus has precipitated a worldwide pandemic, posing a substantial threat to human lives. Growing evidence suggests that SARS-CoV-2 may severely affect the CNS and respiratory system. The current prevalence of clinical neurological issues associated with SARS-CoV-2 has raised significant concerns. However, there needs to be a more comprehensive understanding of the specific pathways by which SARS-CoV-2 enters the nervous system. Based on the available evidence, this review focuses on the clinical neurological manifestations of SARS-CoV-2 and the possible mechanisms by which SARS-CoV-2 invades the brain.

The Cardiac Comeback-Beating Stronger: Exploring the Remarkable Resilience of the Heart in COVID-19 Recovery through Cardiac Autonomic Analysis

Background and Objectives: Analyzing the cardiac autonomic function in COVID-19 patients can provide insights into the impact of the virus on the heart's regulatory mechanisms and its recovery. The autonomic nervous system plays a crucial role in regulating the heart's functions, such as heart rate, blood pressure, and cardiac output. This study aimed to investigate the impact of COVID-19 on heart rate variability (HRV) during a 6-min walk test (6MWT). Materials and Methods: The study included 74 participants, consisting of 37 individuals who had recovered from mild to moderate COVID-19 and 37 healthy controls. The study assessed heart rate variability (HRV) and blood pressure both before and after a 6-min walk test (6MWT). Results: The study found significant differences in a few time domains (SDNN and pNN50) and all frequency domain measures, whereas there were no significant differences in demographic characteristics or blood pressure between COVID-19-recovered individuals and healthy controls at rest. There were significant 6MWT effects on average HR, time-domain (SDNN and pNN50) measures of HRV, and all frequency domain measures of HRV. A significant group × 6MWT interaction was found for SDNN, pNN50, total power, Ln total power, LF, HF, Ln LF, Ln HF, and LF nu. Conclusions: Cardiac Autonomic analysis through HRV is essential to ensure the continued health and well-being of COVID-19 survivors and to minimize the potential long-term impacts of the disease on their cardiovascular system. This suggests that HRV analysis during the recovery phase following exercise could serve as a valuable tool for evaluating the physiological effects of COVID-19 and monitoring the recovery process.

SARS-CoV-2 accessory proteins involvement in inflammatory and profibrotic processes through IL11 signaling

SARS-CoV-2, the cause of the COVID-19 pandemic, possesses eleven accessory proteins encoded in its genome. Their roles during infection are still not completely understood. In this study, transcriptomics analysis revealed that both WNT5A and IL11 were significantly up-regulated in A549 cells expressing individual accessory proteins ORF6, ORF8, ORF9b or ORF9c from SARS-CoV-2 (Wuhan-Hu-1 isolate). IL11 is a member of the IL6 family of cytokines. IL11 signaling-related genes were also differentially expressed. Bioinformatics analysis disclosed that both WNT5A and IL11 were involved in pulmonary fibrosis idiopathic disease and functional assays confirmed their association with profibrotic cell responses. Subsequently, data comparison with lung cell lines infected with SARS-CoV-2 or lung biopsies from patients with COVID-19, evidenced altered profibrotic gene expression that matched those obtained in this study. Our results show ORF6, ORF8, ORF9b and ORF9c involvement in inflammatory and profibrotic responses. Thus, these accessory proteins could be targeted by new therapies against COVID-19 disease.

In Silico Design of New Dual Inhibitors of SARS-CoV-2 MPRO through Ligand- and Structure-Based Methods

The viral main protease is one of the most attractive targets among all key enzymes involved in the life cycle of SARS-CoV-2. Considering its mechanism of action, both the catalytic and dimerization regions could represent crucial sites for modulating its activity. Dual-binding the SARS-CoV-2 main protease inhibitors could arrest the replication process of the virus by simultaneously preventing dimerization and proteolytic activity. To this aim, in the present work, we identified two series' of small molecules with a significant affinity for SARS-CoV-2 M^PRO, by a hybrid virtual screening protocol, combining ligand- and structure-based approaches with multivariate statistical analysis. The Biotarget Predictor Tool was used to filter a large in-house structural database and select a set of benzo[b]thiophene and benzo[b]furan derivatives. ADME properties were investigated, and induced fit docking studies were performed to confirm the DRUDIT prediction. Principal component analysis and docking protocol at the SARS-CoV-2 M^PRO dimerization site enable the identification of compounds 1b,c,i,l and 2i,l as promising drug molecules, showing favorable dual binding site affinity on SARS-CoV-2 M^PRO.

A Comprehensive Review of Natural Flavonoids with Anti-SARS-CoV-2 Activity

The COVID-19 pandemic caused by SARS-CoV-2 has majorly impacted public health and economies worldwide. Although several effective vaccines and drugs are now used to prevent and treat COVID-19, natural products, especially flavonoids, showed great therapeutic potential early in the pandemic and thus attracted particular attention. Quercetin, baicalein, baicalin, EGCG (epigallocatechin gallate), and luteolin are among the most studied flavonoids in this field. Flavonoids can directly or indirectly exert antiviral activities, such as the inhibition of virus invasion and the replication and inhibition of viral proteases. In addition, flavonoids can modulate the levels of interferon and proinflammatory factors. We have reviewed the previously reported relevant literature researching the pharmacological anti-SARS-CoV-2 activity of flavonoids where structures, classifications, synthetic pathways, and pharmacological effects are summarized. There is no doubt that flavonoids have great potential in the treatment of COVID-19. However, most of the current research is still in the theoretical stage. More studies are recommended to evaluate the efficacy and safety of flavonoids against SARS-CoV-2.

Recent updates on liposomal formulations for detection, prevention and treatment of coronavirus disease (COVID-19)

The unprecedented outbreak of severe acute respiratory syndrome-2 (SARS-CoV-2) worldwide has rendered it one of the most notorious pandemics ever documented in human history. As of November 2022, nearly 626 million cases of infection and over 6.6 million deaths have been reported globally. The scientific community has made significant progress in therapeutics and prevention for the management of coronavirus disease (COVID-19), including the development of vaccines and antiviral agents such as monoclonal antibodies and antiviral drugs. Although many advancements and a plethora of positive results have been obtained and global restrictions are being uplifted, obstacles in efficiently delivering these therapies, such as their rapid clearance, suboptimal biodistribution, and toxicity to organs, have yet to be addressed. To address these drawbacks, researchers have attempted applying nanotechnology-based formulations. Here, we summarized the recent data about COVID-19, its emergence, pathophysiology and life cycle, diagnosis, and currently-available medications. Subsequently, we discussed the progress in lipid nanocarriers, such as liposomes in infection detection and control. This review provides critical insights into the design of the latest liposomal-based formulations for tackling the barriers to detecting, preventing, and treating SARS-CoV-2.

SARS-CoV-2 Related Viral Respiratory Co-Infections: A Narrative Review

Background

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the new coronavirus originating from Wuhan, China, responsible for the illness known as coronavirus disease 2019 (COVID-19). Early experience and the recent literature have shown that co-infection of SARS-CoV-2 with another respiratory virus might occur. Similar symptoms of acute respiratory infections (ARIs) and COVID-19 represent a challenge for diagnostic and therapeutic efficacy and may modify COVID-19 outcomes.

Materials and Methods

We reviewed the literature on the epidemic pattern and major learning points on important aspects of SARS-CoV-2-related viral respiratory co-infections during the COVID-19 pandemic. Databases such as PubMed, Scopus, Science Direct, and Google Scholar were used to conduct a comprehensive search.

Results

The circulation of respiratory viruses changed as the COVID-19 epidemic continues. Phenomena like viral interference, resource competition, and differences in virus-host range might explain why simultaneous viral respiratory infections have seemed to vanish with the spread of SARS-CoV-2.

Conclusion

Key research to be conducted during this pandemic should include the simultaneous screening of other respiratory pathogens with many available commercial platforms for transmission containment and appropriate clinical management.

Targeting SARS-CoV-2 Main Protease for Treatment of COVID-19: Covalent Inhibitors Structure-Activity Relationship Insights and Evolution Perspectives

The viral main protease is one of the most attractive targets among all key enzymes involved in the SARS-CoV-2 life cycle. Covalent inhibition of the cysteine145 of SARS-CoV-2 MPRO with selective antiviral drugs will arrest the replication process of the virus without affecting human catalytic pathways. In this Perspective, we analyzed the in silico, in vitro, and in vivo data of the most representative examples of covalent SARS-CoV-2 MPRO inhibitors reported in the literature to date. In particular, the studied molecules were classified into eight different categories according to their reactive electrophilic warheads, highlighting the differences between their reversible/irreversible mechanism of inhibition. Furthermore, the analyses of the most recurrent pharmacophoric moieties and stereochemistry of chiral carbons were reported. The analyses of noncovalent and covalent in silico protocols, provided in this Perspective, would be useful for the scientific community to discover new and more efficient covalent SARS-CoV-2 MPRO inhibitors.

Insights into COVID-19 vaccines development: Translation from benchside to bedside

Over the past decades, the rapid pace of vaccine development saved 37 million lives, mostly children. The ongoing corona virus disease (COVID-19) pandemic caused the death of more than 4 million worldwide. During 2020, to encounter the pandemic, scientists developed more than 300 vaccines projects against SARS-CoV (severe acute respiratory syndrome coronavirus 2). In 2021, the results emerging from the clinical trials led to the approval and rollout of few vaccines in different countries. To date, at least one dose of a COVID-19 vaccine has been received by more than 3.81 billion people worldwide, equal to about 49.7 percent of the world population. This review was written to the aim of providing a snapshot of COVID-19 disease, highlighting the well-known vaccines, and, finally understanding the effect of mix and match vaccines from different types.

Conserved protein targets for developing pan-coronavirus drugs based on sequence and 3D structure similarity analyses

There are 7 known human pathogenic coronaviruses, which are HCoV-229E, HCoV-OC43, HCoV-NL63, HCoV-HKU1, MERS-CoV, SARS-CoV and SARS-CoV-2. While SARS-CoV-2 is currently caused a severe epidemic, experts believe that new pathogenic coronavirus would emerge in the future. Therefore, developing broad-spectrum anti-coronavirus drugs is of great significance. In this study, we performed protein sequence and three-dimensional structure analyses for all the 20 virus-encoded proteins across all the 7 coronaviruses, with the purpose to identify highly conserved proteins and binding sites for developing pan-coronavirus drugs. We found that nsp5, nsp10, nsp12, nsp13, nsp14, and nsp16 are highly conserved both in protein sequences (with average identity percentage higher than 52%, average amino acid conservation scores higher than 5.2) and binding pockets (with average amino acid conservation scores higher than 5.8). We also performed the similarity comparison between these 6 proteins and all the human proteins, and found that all the 6 proteins have similarity less than 25%, indicating that the drugs targeting the 6 proteins should have little interference of human protein function. Accordingly, we suggest that nsp5, nsp10, nsp12, nsp13, nsp14, and nsp16 are potential targets for pan-coronavirus drug development.

SARS-CoV-2-mediated evasion strategies for antiviral interferon pathways

With global expansion of the COVID-19 pandemic and the emergence of new variants, extensive efforts have been made to develop highly effective antiviral drugs and vaccines against SARS-CoV-2. The interactions of coronaviruses with host antiviral interferon pathways ultimately determine successful viral replication and SARS-CoV-2-induced pathogenesis. Innate immune receptors play an essential role in host defense against SARS-CoV-2 via the induction of IFN production and signaling. Here, we summarize the recent advances in innate immune sensing mechanisms of SARS-CoV-2 and various strategies by which SARS-CoV-2 antagonizes antiviral innate immune signaling pathways, with a particular focus on mechanisms utilized by multiple SARS-CoV-2 proteins to evade interferon induction and signaling in host cell. Understanding the underlying immune evasion mechanisms of SARS-CoV-2 is essential for the improvement of vaccines and therapeutic strategies.

Infection and Severity of COVID-19 Infection Among Healthcare Workers: A Report from Egypt

Backgrounds & Aim: Coronavirus disease 2019 (COVID-19) is a severe acute respiratory syndrome caused by Coronavirus. Knowledge of the fate of infection and risk factors among health care workers is essential to enforce special infection control measures. We aimed to determine the percentage of COVID-19 infection and the associated risk factors as well as the predictors of COVID- 19 among health care workers in Assiut University Hospital.

METHODS

A cross-sectional study was performed that included one hundred health care workers that were confirmed by PCR to be COVID-19 cases admitted to Assiut University Hospital over six months between May 2020 and November 2020. All participants were subjected to thorough history taking and full clinical examination as well as investigations.

RESULTS

Out of the 100 HCWs enrolled in the study, 52% were males, 26% were obese, 68% were doctors, and 38% were from the medical department. Fourteen percent of healthcare workers were admitted to ICU, of which 93% were cured. The predictors for severity of cases were as follows: being a doctor OR (6.804) P=0.037, old age OR (1.179) P=0.000, and hospital stay OR (0.838) P=0.015.

CONCLUSION

Health care workers are at risk for severe COVID-19 infection. Being a doctor, old age, and duration of hospitalization were the predictors for the severity of cases of health care workers.

[Proteomic saliva assay in patients with COVID-19]

THE AIM OF THE STUDY

Was to perform proteomic saliva assay in order to reveal mechanisms of the oral pathology caused by COVID-19.

MATERIALS AND METHODS

Proteomic analysis was performed to compare saliva proteins profile in healthy individuals (10 samples) and patients with COVID-19 (30 samples).

RESULTS

The obtained results of the saliva samples study in patients with COVID-19 indicate activation in the oral tissues the pathways of the cell renewal, apoptosis, DNA exchange processes and chromatin remodelling; there are also marked signs of immune response reactivation and immunostimulation.

CONCLUSION

Of all the proteins presented, the saliva of patients with COVID-19 33 proteins have an intersection with GO-annotated proteins of inflammation and epithelial cornification.

A fractional-order model of COVID-19 considering the fear effect of the media and social networks on the community

Since December 2019, the world has experienced from a virus, known as Covid-19, that is highly transmittable and is now spread worldwide. Many mathematical models and studies have been implemented to work on the infection and transmission risks. Besides the virus's transmission effect, another discussion appears in the community: the fear effect. People who have never heard about coronavirus, face every day uncertain and different information regarding the effect of the virus and the daily death rates from sources like the media, the medical institutions or organizations. Thus, the fear of the virus in the community can possibly reach the point that people become scared and confused about information polluted from different networks with long-term trend discussions. In this work, we use the Routh-Hurwitz Criteria to analyze the local stability of two essential critical points: the disease-free and the co-existing critical point. Using the discretization process, our analysis have shown that one should distinguish between the spread of "awareness" or "fear" in the community through the media and others to control the virus's transmission. Finally, we conclude our theoretical findings with numerical simulations.

A fractional-order model of COVID-19 considering the fear effect of the media and social networks on the community

Since December 2019, the world has experienced from a virus, known as Covid-19, that is highly transmittable and is now spread worldwide. Many mathematical models and studies have been implemented to work on the infection and transmission risks. Besides the virus's transmission effect, another discussion appears in the community: the fear effect. People who have never heard about coronavirus, face every day uncertain and different information regarding the effect of the virus and the daily death rates from sources like the media, the medical institutions or organizations. Thus, the fear of the virus in the community can possibly reach the point that people become scared and confused about information polluted from different networks with long-term trend discussions. In this work, we use the Routh-Hurwitz Criteria to analyze the local stability of two essential critical points: the disease-free and the co-existing critical point. Using the discretization process, our analysis have shown that one should distinguish between the spread of "awareness" or "fear" in the community through the media and others to control the virus's transmission. Finally, we conclude our theoretical findings with numerical simulations.

Molecular Level Dissection of Critical Spike Mutations in SARS-CoV-2 Variants of Concern (VOCs): A Simplified Review

SARS-CoV-2 virus during its spread in the last one and half year has picked up critical changes in its genetic code i.e. mutations, which have leads to deleterious epidemiological characteristics. Due to critical role of spike protein in cell entry and pathogenesis, mutations in spike regions have been reported to enhance transmissibility, disease severity, possible escape from vaccine-induced immune response and reduced diagnostic sensitivity/specificity. Considering the structure-function impact of mutations, understanding the molecular details of these key mutations of newly emerged variants/lineages is of urgent concern. In this review, we have explored the literature on key spike mutations harbored by alpha, beta, gamma and delta 'variants of concern' (VOCs) and discussed their molecular consequences in the context of resultant virus biology. Commonly all these VOCs i.e. B.1.1.7, B.1.351, P.1 and B.1.617.2 lineages have decisive mutation in Receptor Binding Motif (RBM) region and/or region around Furin cleavage site (FCS) of spike protein. In general, mutation induced disruption of intra-molecular interaction enhances molecular flexibility leading to exposure of spike protein surface in these lineages to make it accessible for inter-molecular interaction with hACE2. A disruption of spike antigen-antibody inter-molecular interactions in epitope region due to the chemical nature of substituting amino acid hampers the neutralization efficacy. Simplified surveillance of mutation induced changes and their consequences at molecular level can contribute in rationalizing mutation's impact on virus biology. It is believed that molecular level dissection of these key spike mutation will assist the future investigations for a more resilient outcome against severity of COVID-19.

SARS-CoV-2 Cellular Entry Is Independent of the ACE2 Cytoplasmic Domain Signaling

Recently emerged severe acute respiratory syndrome coronavirus (SARS-CoV)-1 and -2 initiate virus infection by binding of their spike glycoprotein with the cell-surface receptor angiotensin-converting enzyme 2 (ACE2) and enter into the host cells mainly via the clathrin-mediated endocytosis pathway. However, the internalization process post attachment with the receptor is not clear for both SARS-CoV-1 and -2. Understanding the cellular factor/s or pathways used by these CoVs for internalization might provide insights into viral pathogenesis, transmission, and development of novel therapeutics. Here, we demonstrated that the cytoplasmic tail of ACE2 is not essential for the entry of SARS-CoV-1 and -2 by using bioinformatics, mutational, confocal imaging, and pseudotyped SARS-CoVs infection studies. ACE2 cytoplasmic domain (cytACE2) contains a conserved internalization motif and eight putative phosphorylation sites. Complete cytoplasmic domain deleted ACE2 (∆cytACE2) was properly synthesized and presented on the surface of HEK293T and BHK21 cells like wtACE2. The SARS-CoVs S1 or RBD of spike protein binds and colocalizes with the receptors followed by internalization into the host cells. Moreover, pseudotyped SARS-CoVs entered into wtACE2- and ∆cytACE2-transfected cells but not into dipeptidyl peptidase 4 (DPP4)-expressing cells. Their entry was significantly inhibited by treatment with dynasore, a dynamin inhibitor, and NH₄Cl, an endosomal acidification inhibitor. Furthermore, SARS-CoV antibodies and the soluble form of ACE2-treated pseudotyped SARS-CoVs were unable to enter the wtACE2 and ∆cytACE2-expressing cells. Altogether, our data show that ACE2 cytoplasmic domain signaling is not essential for the entry of SARS-CoV-1 and -2 and that SARS-CoVs entry might be mediated via known/unknown host factor/s.

Heparan Sulfate Proteoglycans in Viral Infection and Treatment: A Special Focus on SARS-CoV-2

Heparan sulfate proteoglycans (HSPGs) encompass a group of glycoproteins composed of unbranched negatively charged heparan sulfate (HS) chains covalently attached to a core protein. The complex HSPG biosynthetic machinery generates an extraordinary structural variety of HS chains that enable them to bind a plethora of ligands, including growth factors, morphogens, cytokines, chemokines, enzymes, matrix proteins, and bacterial and viral pathogens. These interactions translate into key regulatory activity of HSPGs on a wide range of cellular processes such as receptor activation and signaling, cytoskeleton assembly, extracellular matrix remodeling, endocytosis, cell-cell crosstalk, and others. Due to their ubiquitous expression within tissues and their large functional repertoire, HSPGs are involved in many physiopathological processes; thus, they have emerged as valuable targets for the therapy of many human diseases. Among their functions, HSPGs assist many viruses in invading host cells at various steps of their life cycle. Viruses utilize HSPGs for the attachment to the host cell, internalization, intracellular trafficking, egress, and spread. Recently, HSPG involvement in the pathogenesis of SARS-CoV-2 infection has been established. Here, we summarize the current knowledge on the molecular mechanisms underlying HSPG/SARS-CoV-2 interaction and downstream effects, and we provide an overview of the HSPG-based therapeutic strategies that could be used to combat such a fearsome virus.

Oral Mucosa, Saliva, and COVID-19 Infection in Oral Health Care

The SARS-CoV-2 virus has shaken the globe with an ongoing pandemic of COVID-19 and has set challenges to every corner of the modern health care setting. The oral mucosa and saliva are high risk sites for higher viral loads and dental health care professionals are considered a high risk group. COVID-19-induced oral lesions and loss of taste and smell are common clinical complaints in the dental health care setting. The SARS-CoV-2 virus has been found to cause a wide range of non-specific oral mucosal lesions, but the specific diagnosis of these mucocutaneous lesions as COVID-19 lesions will facilitate the prevention of SARS-CoV-2 in dental health care settings and aid in proper patient management. The reported loss of taste and smell needs further investigation at the receptor level as it will give new insights into SARS-CoV-2 pathogenicity. The high yield of virus in the salivary secretion is a common finding in this infection and ongoing research is focusing on developing saliva as a rapid diagnostic fluid in COVID-19. In this review, we discuss the significance of oral mucosa, saliva and the relevance of the COVID-19 pandemic in dentistry.

Seroprevalence and Risk Factors for Exposure to Equine Coronavirus in Apparently Healthy Horses in Israel

Simple Summary

Equine coronavirus (ECoV) is a β-coronavirus that, together with other coronaviruses, are pathogenic to both human and animals, as seen in the recent COVID-19 pandemic. ECoV is considered as a diarrheic pathogen in foals and is included in the list of viral causes of enteritis. During the last decade, outbreaks of ECoV were reported in adult horses in the USA, EU and Japan. In Israel, other coronaviruses were reported in cattle, camels and in humans; however, coronaviruses have not been reported in horses. In this study, we aimed to determine the exposure of healthy horses to ECoV and determine the selected risk factors for infection. For this purpose, serum samples were collected from 333 healthy horses, 41 (12.3%) of which had anti-ECoV antibodies. Seropositive horses were found in more than half (58.6%) of the farms and horses located in central Israel were more likely to be positive. ECoV should be included in the differential diagnosis list of pathogens in cases of adult horses with acute onset of anorexia, lethargy, fever and gastrointestinal signs in Israel.

Abstract

Equine coronavirus (ECoV) infection is the cause of an emerging enteric disease of adult horses. Outbreaks have been reported in the USA, EU and Japan, as well as sporadic cases in the UK and Saudi Arabia. Infection of ECoV in horses in Israel has never been reported, and the risk of exposure is unknown. Importation and exportation of horses from and into Israel may have increased the exposure of horses in Israel to ECoV. While the disease is mostly self-limiting, with or without supportive treatment, severe complications may occur in some animals, and healthy carriers may pose a risk of infection to other horses. This study was set to evaluate the risk of exposure to ECoV of horses in Israel by using a previously validated, S1-based enzyme-linked immunosorbent assay (ELISA). A total of 41 out of 333 horses (12.3%) were seropositive. Exposure to ECoV was detected in 17 of 29 farms (58.6%) and the seroprevalence varied between 0 and 37.5% amongst farms. The only factor found to be significantly associated with ECoV exposure in the multivariable model was the geographical area (p < 0.001). ECoV should be included in the differential diagnosis list of pathogens in cases of adult horses with anorexia, lethargy, fever and gastrointestinal signs in Israel.

An Overview of Spike Surface Glycoprotein in Severe Acute Respiratory Syndrome-Coronavirus

The novel coronavirus originated in December 2019 in Hubei, China. This contagious disease named as COVID-19 resulted in a massive expansion within 6 months by spreading to more than 213 countries. Despite the availability of antiviral drugs for the treatment of various viral infections, it was concluded by the WHO that there is no medicine to treat novel CoV, SARS-CoV-2. It has been confirmed that SARS-COV-2 is the most highly virulent human coronavirus and occupies the third position following SARS and MERS with the highest mortality rate. The genetic assembly of SARS-CoV-2 is segmented into structural and non-structural proteins, of which two-thirds of the viral genome encodes non-structural proteins and the remaining genome encodes structural proteins. The most predominant structural proteins that make up SARS-CoV-2 include spike surface glycoproteins (S), membrane proteins (M), envelope proteins (E), and nucleocapsid proteins (N). This review will focus on one of the four major structural proteins in the CoV assembly, the spike, which is involved in host cell recognition and the fusion process. The monomer disintegrates into S1 and S2 subunits with the S1 domain necessitating binding of the virus to its host cell receptor and the S2 domain mediating the viral fusion. On viral infection by the host, the S protein is further cleaved by the protease enzyme to two major subdomains S1/S2. Spike is proven to be an interesting target for developing vaccines and in particular, the RBD-single chain dimer has shown initial success. The availability of small molecules and peptidic inhibitors for host cell receptors is briefly discussed. The development of new molecules and therapeutic druggable targets for SARS-CoV-2 is of global importance. Attacking the virus employing multiple targets and strategies is the best way to inhibit the virus. This article will appeal to researchers in understanding the structural and biological aspects of the S protein in the field of drug design and discovery.

A comprehensive review of SARS-CoV-2 genetic mutations and lessons from animal coronavirus recombination in one health perspective

SARS-CoV-2 was originated from zoonotic coronaviruses and confirmed as a novel beta-coronavirus, which causes serious respiratory illness such as pneumonia and lung failure, COVID-19. In this review, we describe the genetic characteristics of SARS-CoV-2, including types of mutation, and molecular epidemiology, highlighting its key difference from animal coronaviruses. We further summarized the current knowledge on clinical, genetic, and pathological features of several animal coronaviruses and compared them with SARS-CoV-2, as well as recent evidences of interspecies transmission and recombination of animal coronaviruses to provide a better understanding of SARS-CoV-2 infection in One Health perspectives. We also discuss the potential wildlife hosts and zoonotic origin of this emerging virus in detail, that may help mitigate the spread and damages caused by the disease.