Overview of lethal human coronaviruses

Glycan Nanostructures of Human Coronaviruses

Human coronaviruses present a substantial global disease burden, causing damage to populations’ health, economy, and social well-being. Glycans are one of the main structural components of all microbes and organismic structures, including viruses—playing multiple essential roles in virus infection and immunity. Studying and understanding virus glycans at the nanoscale provide new insights into the diagnosis and treatment of viruses. Glycan nanostructures are considered potential targets for molecular diagnosis, antiviral therapeutics, and the development of vaccines. This review article describes glycan nanostructures (eg, glycoproteins and glycolipids) that exist in cells, subcellular structures, and microbes. We detail the structure, characterization, synthesis, and functions of virus glycans. Furthermore, we describe the glycan nanostructures of different human coronaviruses, such as human coronavirus 229E (HCoV-229E), human coronavirus OC43 (HCoV-OC43), severe acute respiratory syndrome-associated coronavirus (SARS-CoV), human coronavirus NL63 (HCoV-NL63), human coronavirus HKU1 (HCoV-HKU1), the Middle East respiratory syndrome-associated coronavirus (MERS-CoV), and how glycan nanotechnology can be useful to prevent and combat human coronaviruses infections, along with possibilities that are not yet explored.

A Comparison of the Clinical, Viral, Pathologic, and Immunologic Features of Severe Acute Respiratory Syndrome (SARS), Middle East Respiratory Syndrome (MERS), and Coronavirus 2019 (COVID-19) Diseases

CONTEXT

-The purpose of this review is to compare three coronavirus diseases: severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and coronavirus disease 2019 (COVID-19) caused by SARS-CoV, MERS-CoV, and SARS-CoV-2 viruses, respectively.

OBJECTIVE

-To cover the following topics: clinical considerations, viral characteristics, pathology, immune response, pathogenesis, and the prognosis associated with each coronavirus human disease in humans.

DATA SOURCES

-Clinically, flu-like symptoms are usual at the time of presentation for all 3 diseases, but these vary from asymptomatic to severe multi-system involvement. The pathology associated with symptomatic SARS and COVID-19 has been well described, the most prominent of which is diffuse alveolar damage (DAD). The immune response to each of these viruses is highly complex and includes both humoral and cellular components that can have a significant impact on prognosis. In severe cases of COVID-19, a dysregulated innate host immune system can initiate a hyperinflammatory syndrome dominated by endothelial dysfunction that can lead to a hypercoagulable state with microthrombi, resulting in a systemic micro- and macro-vascular disease.

CONCLUSIONS

-The SARS and MERS epidemics have been limited, involving 7,500 and 2,500 individuals, respectively. In contrast, COVID-19 has resulted in a worldwide pandemic with over 177 million cases and 3.9 million deaths as of June 15, 2021, and fatality rates ranging from <0.1% to ~10% depending upon the country. Ending on a positive note, the development of a number of vaccines, at least six of which now are in clinical use, should mitigate and eventually control the devastating COVID-19 pandemic.

Dynamics of host immune responses to SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the most recent global health threat, is spreading throughout the world with worrisome speed, and the current wave of coronavirus disease 2019 (COVID-19) seems to have no mercy. While this mysterious virus challenges our ability to control viral infections, our opportunities to control the COVID-19 pandemic are gradually fading. Currently, pandemic management relies on preventive interventions. Although prevention is a good strategy to mitigate SARS-CoV-2 transmission, it still cannot be considered an absolute solution to eliminate this pandemic. Currently, developing a potent immunity against this viral infection seems to be the most promising strategy to drive down this ongoing global tragedy. However, with the emergence of new challenges in the context of immune responses to COVID-19, the road to control this devastating pandemic seems bumpier; thus, it is pivotal to characterize the dynamics of host immune responses to COVID-19, in order to develop efficient prophylactic and therapeutic tools. This begs the question of whether the effector mechanisms of the immune system are indeed potent or a possible contributing factor to developing more severe and lethal forms of COVID-19. In this review, the possible role of the immunopathologic phenomena including antibody-dependent enhancement, cytokine storm, and original antigenic sin in severity and mortality of COVID-19 will be discussed.

Comprehensive Survey of Using Machine Learning in the COVID-19 Pandemic

Since December 2019, the global health population has faced the rapid spreading of coronavirus disease (COVID-19). With the incremental acceleration of the number of infected cases, the World Health Organization (WHO) has reported COVID-19 as an epidemic that puts a heavy burden on healthcare sectors in almost every country. The potential of artificial intelligence (AI) in this context is difficult to ignore. AI companies have been racing to develop innovative tools that contribute to arm the world against this pandemic and minimize the disruption that it may cause. The main objective of this study is to survey the decisive role of AI as a technology used to fight against the COVID-19 pandemic. Five significant applications of AI for COVID-19 were found, including (1) COVID-19 diagnosis using various data types (e.g., images, sound, and text); (2) estimation of the possible future spread of the disease based on the current confirmed cases; (3) association between COVID-19 infection and patient characteristics; (4) vaccine development and drug interaction; and (5) development of supporting applications. This study also introduces a comparison between current COVID-19 datasets. Based on the limitations of the current literature, this review highlights the open research challenges that could inspire the future application of AI in COVID-19.

A critical review on SARS-CoV-2 infectivity in water and wastewater. What do we know?

The COVID-19 outbreak circulating the world is far from being controlled, and possible contamination routes are still being studied. There are no confirmed cases yet, but little is known about the infection possibility via contact with sewage or contaminated water as well as with aerosols generated during the pumping and treatment of these aqueous matrices. Therefore, this article presents a literature review on the detection of SARS-CoV-2 in human excreta and its pathways through the sewer system and wastewater treatment plants until it reaches the water bodies, highlighting their occurrence and infectivity in sewage and natural water. Research lines are still indicated, which we believe are important for improving the detection, quantification, and mainly the infectivity analyzes of SARS-CoV-2 and other enveloped viruses in sewage and natural water. In fact, up till now, no case of transmission via contact with sewage or contaminated water has been reported and the few studies conducted with these aqueous matrices have not detected infectious viruses. On the other hand, studies are showing that SARS-CoV-2 can remain viable, i.e., infectious, for up to 4.3 and 6 days in sewage and water, respectively, and that other species of coronavirus may remain viable in these aqueous matrices for more than one year, depending on the sample conditions. These are strong pieces of evidence that the contamination mediated by contact with sewage or contaminated water cannot be ruled out, even because other more resistant and infectious mutations of SARS-CoV-2 may appear.

SARS-CoV-2: Origin, Evolution, and Targeting Inhibition

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused an outbreak in Wuhan city, China and quickly spread worldwide. Currently, there are no specific drugs or antibodies that claim to cure severe acute respiratory diseases. For SARS-CoV-2, the spike (S) protein recognizes and binds to the angiotensin converting enzyme 2 (ACE2) receptor, allowing viral RNA to enter the host cell. The main protease (Mpro) is involved in the proteolytic process for mature non-structural proteins, and RNA-dependent RNA polymerase (RdRp) is responsible for the viral genome replication and transcription processes. Owing to the pivotal physiological roles in viral invasion and replication, S protein, Mpro, RdRp are regarded as the main therapeutic targets for coronavirus disease 2019 (COVID-19). In this review, we carried out an evolutionary analysis of SARS-CoV-2 in comparison with other mammal-infecting coronaviruses that have sprung up in the past few decades and described the pathogenic mechanism of SARS-CoV-2. We displayed the structural details of S protein, Mpro, and RdRp, as well as their complex structures with different chemical inhibitors or antibodies. Structural comparisons showed that some neutralizing antibodies and small molecule inhibitors could inhibit S protein, Mpro, or RdRp. Moreover, we analyzed the structural differences between SARS-CoV-2 ancestral S protein and D614G mutant, which led to a second wave of infection during the recent pandemic. In this context, we outline the methods that might potentially help cure COVID-19 and provide a summary of effective chemical molecules and neutralizing antibodies.

Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection

Background

The spread of a novel severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) has affected both the public health and the global economy. The current study was aimed at analysing the genetic sequence of this highly contagious corona virus from an evolutionary perspective, comparing the genetic variation features of different geographic strains, and identifying the key miRNAs as well as their gene targets from the transcriptome data of infected lung tissues.

Methods

A multilevel robust computational analysis was undertaken for viral genetic sequence alignment, phylogram construction, genome-wide transcriptome data interpretation of virus-infected lung tissues, miRNA mapping, and functional biology networking.

Results

Our findings show both genetic similarities as well as notable differences in the S protein length among SARS-CoV-1, SARS-CoV-2 and MERS viruses. All SARS-CoV-2 strains showed a high genetic similarity with the parent Wuhan strain, but Saudi Arabian, South African, USA, Russia and New Zealand strains carry 3 additional genetic variations like P333L (RNA -dependant RNA polymerase), D614G (spike), and P4715L (ORF1ab). The infected lung tissues demonstrated the upregulation of 282 (56.51%) antiviral defensive response pathway genes and downregulation of 217 (43.48%) genes involved in autophagy and lung repair pathways. By miRNA mapping, 4 key miRNAs (hsa-miR-342-5p, hsa-miR-432-5p, hsa-miR-98-5p and hsa-miR-17-5p), targeting multiple host genes (MYC, IL6, ICAM1 and VEGFA) as well as SARS-CoV2 gene (ORF1ab) were identified.

Conclusion

Systems biology methods offer a new perspective in understanding the molecular basis for the faster spread of SARS-CoV-2 infection. The antiviral miRNAs identified in this study may aid in the ongoing search for novel personalized therapeutic avenues for COVID patients.

Developing a Paper-Based Antigen Assay to Differentiate between Coronaviruses and SARS-CoV-2 Spike Variants

COVID-19 first appeared in December of 2019 in Wuhan, China. Since then, it has become a global pandemic. A robust and scalable diagnostics strategy is crucial for containing and monitoring the pandemic. RT-PCR is a known, reliable method for COVID-19 diagnostics, which can differentiate between SARS-CoV-2 and other viruses. However, PCR is location-dependent, time-consuming, and relatively expensive. Thus, there is a need for a more flexible method, which may be produced in an off-the-shelf format and distributed more widely. Paper-based immunoassays can fulfill this function. Here, we present the first steps toward a paper-based test, which can differentiate between different spike proteins of various coronaviruses, SARS-CoV-1, SARS-CoV-2, and CoV-HKU1, with negligible cross-reactivity for HCoV-OC43 and HCoV-229E in a single assay, which takes less than 30 min. Furthermore, our test can distinguish between fractions of the same spike protein. This is done by an altered assay design with four test line locations where each antigen builds a unique, identifiable binding pattern. The effect of several factors, such as running media, immunoprobe concentration, and antigen interference, is considered. We find that running media has a significant effect on the final binding pattern where human saliva provides results while human serum leads to the lowest signal quality.

Anti-Coronavirus Vaccines: Past Investigations on SARS-CoV-1 and MERS-CoV, the Approved Vaccines from BioNTech/Pfizer, Moderna, Oxford/AstraZeneca and others under Development Against SARS-CoV-2 Infection

The aim of this review article is to summarize the knowledge available to date on prophylaxis achievements to fight against Coronavirus. This work will give an overview of what is reported in the most recent literature on vaccines (under investigation or already developed like BNT162b2, mRNA-1273, and ChAdOx1-S) effective against the most pathogenic Coronaviruses (SARS-CoV-1, MERS-CoV-1, and SARS-CoV-2), with of course particular attention paid to those under development or already in use to combat the current COVID-19 (COronaVIrus Disease 19) pandemic. Our main objective is to make a contribution to the comprehension, additionally at a molecular level, of what is currently ready for anti-SARS-CoV-2 prophylactic intervention, as well as to provide the reader with an overall picture of the most innovative approaches for the development of vaccines that could be of general utility in the fight against the most pathogenic Coronaviruses.

Exploring SARS-CoV-2 Spikes Glycoproteins for Designing Potential Antiviral Targets

Till today, the globe is still struggling with the newly emerging infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and known as coronavirus disease 2019 (COVID-19). It has resulted in multiple fatalities from SARSs all around the world. A year after the global pandemic, the World Health Organization (WHO) has reported more than 79 million confirmed cases of COVID-19 and over 1.7 million deaths, making it one of the worst and most difficult pandemics encompassed in the modern history. The ongoing triad of escalating infections, mortality, and economic loss has urgently called for recognizing SARS-CoV-2 cell entry mechanisms as a crucial step in the initial stages of infection and to which possible interventional strategies should be targeted. To mediate host cell infections, Coronaviruses utilize the immunogenic studded spikes glycoproteins on its surface as a key factor for attachment, fusion, and entrance to host cells. Herein, we shed the light on a potential strategy involving disruption of SARS-CoV-2 S protein interaction with host cell receptors through design of neutralizing antibodies targeting receptor binding domain in S1 subunit, small peptide inhibitors, peptide fusion inhibitors against S2, host cell angiotensin converting enzymes 2 (ACE2), and protease inhibitors, aiming to pave the way for controlling viral cell entrance. In this review, we also highlight the recent research advances in the antiviral drugs that target the highly exposed spike protein, aiming to stem the COVID-19 pandemic.

Type-I interferon signatures in SARS-CoV-2 infected Huh7 cells

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes Coronavirus disease 2019 (COVID-19) has caused a global health emergency. A key feature of COVID-19 is dysregulated interferon-response. Type-I interferon (IFN-I) is one of the earliest antiviral innate immune responses following viral infection and plays a significant role in the pathogenesis of SARS-CoV-2. In this study, using a proteomics-based approach, we identified that SARS-CoV-2 infection induces delayed and dysregulated IFN-I signaling in Huh7 cells. We demonstrate that SARS-CoV-2 is able to inhibit RIG-I mediated IFN-β production. Our results also confirm the recent findings that IFN-I pretreatment is able to reduce the susceptibility of Huh7 cells to SARS-CoV-2, but not post-treatment. Moreover, senescent Huh7 cells, in spite of showing accentuated IFN-I response were more susceptible to SARS-CoV-2 infection, and the virus effectively inhibited IFIT1 in these cells. Finally, proteomic comparison between SARS-CoV-2, SARS-CoV, and MERS-CoV revealed a distinct differential regulatory signature of interferon-related proteins emphasizing that therapeutic strategies based on observations in SARS-CoV and MERS-CoV should be used with caution. Our findings provide a better understanding of SARS-CoV-2 regulation of cellular interferon response and a perspective on its use as a treatment. Investigation of different interferon-stimulated genes and their role in the inhibition of SARS-CoV-2 pathogenesis may direct novel antiviral strategies.

Antiviral peptides against Coronaviridae family: A review

The Coronaviridae family comprises large enveloped single-stranded RNA viruses. The known human-infecting coronaviruses; severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), novel SARS-CoV-2, human coronavirus (HCoV)-NL63, HCoV-229E, HCoV-OC43 and HKU1 cause mild to severe respiratory infections. The viral diseases induced by mammalian and avian viruses from Coronaviridae family pose significant economic and public health burdens. Due to increasing reports of viral resistance, co-infections and the emergence of viral epidemics such as COVID-19, available antiviral drugs show low or no efficacy, and the production of new treatments or vaccines are also challenging. Therefore, demand for the development of novel antivirals has considerably increased. In recent years, antiviral peptides have generated increasing interest as they are from natural and computational sources, are highly specific and effective, and possess the broad-spectrum activity with minimum side effects. Here, we have made an effort to compile and review the antiviral peptides with activity against Coronaviridae family viruses. They were divided into different categories according to their action mechanisms, including binding/attachment inhibitors, fusion and entry inhibitors, viral enzyme inhibitors, replication inhibitors and the peptides with direct and indirect effects on the viruses. Reported studies suggest optimism with regard to the design and production of therapeutically promising antiviral drugs. This review aims to summarize data relating to antiviral peptides particularly with respect to their applicability for development as novel treatments.

Insights into forsythia honeysuckle (Lianhuaqingwen) capsules: A Chinese herbal medicine repurposed for COVID-19 pandemic

Background

In December 2019, a novel coronavirus, SARS-CoV-2 caused a series of acute atypical respiratory diseases worldwide. However, there is still a lack of drugs with clear curative effects, and the clinical trial research of vaccines has not been completely finished.

Purpose

LH capsules are approved TCM patent medicine that are widely used for the treatment of respiratory tract infectious diseases caused by colds and flu. On April 12, 2020, LH capsules and granules were officially repurposed by the China Food and Drug Administration (CFDA) for patients with mild COVID-19 based on their safety and efficacy demonstrated through multicentre, randomized, controlled clinical trials. We hope to conduct a comprehensive review of it through modern pharmacy methods, and try to explain its possible mechanism.

Methods

Using the full names of LH capsules Lianhuaqingwen, Lianhua Qingwen andSARS-COV-2, COVID-19 as the keywords of the search terms, systemically search for existing related papers in various databases such as Web of Science and PubMed. And completed the collection of clinical data in ClinicalTrials.gov and Chinese Clinical Trial Registry. Last but not least, we have sorted out the anti-inflammatory and antiviral mechanisms of LH capsules through literature and Selleck.

Results

This review systematically sorted out the active ingredients in LH capsules. Furthermore, the related pharmacological and clinical trials of LH capsule on SARS-CoV-2, IAV and IBV were discussed in detail. Moreover, the present review provides the first summary of the potential molecular mechanism of specific substances in LH capsules involved in resistance to SARS-COV-2 infection and the inhibition of cytokine storm syndrome (CSS) caused by IL-6.

Conclusion

This review summarizes the available reports and evidence that support the use of LH capsules as potential drug candidates for the prevention and treatment of COVID-19. However, TCM exerts its effects through multiple targets and multiple pathways, and LH capsules are not an exception. Therefore, the relevant mechanisms need to be further improved and experimentally verified.

Antibodies and Vaccines Target RBD of SARS-CoV-2

The novel human coronavirus, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which gives rise to the coronavirus disease 2019 (COVID-19), has caused a serious threat to global public health. On March 11, 2020, the WHO had officially announced COVID-19 as a pandemic. Therefore, it is vital to find effective and safe neutralizing antibodies and vaccines for COVID-19. The critical neutralizing domain (CND) that is contained in the receptor-binding domain (RBD) of the spike protein (S protein) could lead to a highly potent neutralizing antibody response as well as the cross-protection of other strains of SARS. By using RBD as an antigen, many neutralizing antibodies are isolated that are essential to the therapeutics of COVID-19. Furthermore, a subunit vaccine, which is based on the RBD, is expected to be safer than others, thus the RBD in the S protein is a more important target for vaccine development. In this review, we focus on neutralizing antibodies that are targeting RBD as well as the vaccine based on RBD under current development.

Antibody-Dependent Enhancement and the Critical Pattern of COVID-19: Possibilities and Considerations

Coronavirus disease 2019 (COVID-19), a pandemic infection with profound effects on human society, has challenged our ability to control viral infections. Although at the beginning of the COVID-19 outbreak, the epidemic seemed controllable in Southern Iran, the disease presented a critical pattern as of May 2020. After a few months of the emergence of COVID-19, its severity and mortality increased dramatically. It has been proposed that antibodies produced during previous exposure to local circulating human coronaviruses or possibly severe acute respiratory syndrome coronavirus 2 might contribute to the development of more severe and lethal presentations of COVID-19 possibly by triggering antibody-dependent enhancement. The binding of virions complexed with antibodies to Fcγ receptors on the target cells initiates receptor-mediated signaling events, leading to enhanced expression of inflammatory cytokines and suppression of intracellular antiviral responses at the transcriptome level, followed by endocytosis of the virus and subsequent activation of immune cells. The activated immune cells might accumulate in the lung and promote cytokine storm and lymphopenia. Furthermore, the formation of immune complexes can promote complement activation and subsequent tissue damage. Although there are currently no clinical data to support this hypothesis, a better understanding of these immunopathologic phenomena and their relation to the disease course and severity might give insights into the development of the most efficient prophylactic and therapeutic approaches. This review demonstrates the critical pattern of COVID-19 in Southern Iran and highlights the possible interplay of factors leading to this condition.

Interactions between SARS coronavirus 2 papain-like protease and immune system: A potential drug target for the treatment of COVID-19

Coronaviruses (CoVs) are a large family of respiratory viruses which can cause mild to moderate upper respiratory tract infections. Recently, new coronavirus named as Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has been identified which is a major threat to public health. Innate immune responses play a vital role in a host's defence against viruses. Interestingly, CoVs have evolved elaborate strategies to evade the complex system of sensors and signalling molecules to suppress host immunity. SARS‐CoV‐2 papain‐like protease (PLpro), as an important coronavirus enzyme, regulates viral spread and innate immune responses. SCoV‐2 PLpro is multifunctional enzyme with deubiquitinating (DUB) and deISGylating activity. The PLpro can interact with key regulators in signalling pathways such as STING, NF‐κB, cytokine production, MAPK and TGF‐β and hijack those to block the immune responses. Therefore, the PLpro can be as an important target for the treatment of COVID‐19. Until now, several drugs or compounds have been identified that can inhibit PLpro activity. Here we discuss about the dysregulation effects of PLpro on immune system and drugs that have potential inhibitors for SCoV‐2 PLpro.

Structure- and Ligand-Based in silico Studies towards the Repurposing of Marine Bioactive Compounds to Target SARS-CoV-2

This work was a structured virtual screening for marine bioactive compounds with reported antiviral activities which were subjected to structure-based studies against SARS-CoV-2 co-crystallized proteins. The molecular docking of marine bioactive compounds against the main protease (Mpro, PDB ID: 6lu7 and 6y2f), the spike glycoprotein (PDB ID: 6vsb), and the RNA polymerase (PDB ID: 6m71) of SARS-CoV-2 was performed. Ligand-based approach with the inclusion of rapid overlay chemical structures (ROCS) was also addressed in order to examine the probability of these marine compounds sharing relevance and druggability with the reported drugs. Among the examined marine library, the highest scores in different virtual screening aspects were displayed by compounds with flavonoids core, acyl indole, and pyrrole carboxamide alkaloids. Moreover, a complete overlay with the co-crystallized ligands of Mpro was revealed by sceptrin and debromo-sceptrin. Thalassoilin (A-B) which was found in the Red Sea exhibited the highest binding and similarity outcomes among all target proteins. These data highlight the importance of marine natural metabolites in regard to further studies for discovering new drugs to combat the COVID-19 pandemic.

Recent advances in nanomaterials based biosensors for point of care (PoC) diagnosis of Covid-19 - A minireview

Early diagnosis and ultrahigh sample throughput screening are the need of the hour to control the geological spread of the COVID-19 pandemic. Traditional laboratory tests such as enzyme-linked immunosorbent assay (ELISA), reverse transcription polymerase chain reaction (RT-PCR) and computed tomography are implemented for the detection of COVID-19. However, they are limited by the laborious sample collection and processing procedures, longer wait time for test results and skilled technicians to operate sophisticated facilities. In this context, the point of care (PoC) diagnostic platform has proven to be the prospective approach in addressing the abovementioned challenges. This review emphasizes the mechanism of viral infection spread detailing the host-virus interaction, pathophysiology, and the recent advances in the development of affordable PoC diagnostic platforms for rapid and accurate diagnosis of COVID-19. First, the well-established optical and electrochemical biosensors are discussed. Subsequently, the recent advances in the development of PoC biosensors, including lateral flow immunoassays and other emerging techniques, are highlighted. Finally, a focus on integrating nanotechnology with wearables and smartphones to develop smart nanobiosensors is outlined, which could promote COVID-19 diagnosis accessible to both individuals and the mass population at patient care.

BRD4 targeting nanotherapy prevents lipopolysaccharide induced acute respiratory distress syndrome

Acute respiratory distress syndrome (ARDS) is a life threatening respiratory disease associated with pulmonary edema, alveolar dysfunction, hypoxia, and inflammatory cell accumulation. The most contagious form of COVID-19 associated with ARDS caused by SARS-CoV-2. SARS-CoV-2 majorly produces the cytokine storm and severe lung inflammation and ultimately leads to respiratory failure. ARDS is a complex disease and there is no proper therapeutics for effective therapy. Still, there is a huge scope to identify novel targets to combat respiratory illness. In the current study, we have identified the epigenetic regulating protein BRD4 and developed siRNA based nanomedicine to treat the ARDS. The liposomes were prepared by thin-film hydration method, where BRD4 siRNA complexed with cationic lipid and exhibited 96.24 ± 18.01 nm size and stable even in the presence of RNase. BRD4 siRNA lipoplexes (BRD4-siRNA-LP) inhibited inflammatory cells in lungs and suppressed the lipopolysaccharide (LPS) induced the neutrophil infiltration and mast cell accumulation. Also, BRD4 siRNA based nanomedicine significantly reduced the LPS induced cytokine storm followed by inflammatory signaling pathways. Interestingly, BRD4-siRNA-LP suppressed the LPS-induced p65 and STAT3 nuclear translocation and ameliorated the lung inflammation. Thus, BRD4-siRNA-LP could be a plausible therapeutic option for treating ARDS and might be useful for combating the COVID-19 associated respiratory illness.

Molecular Basis of the Therapeutical Potential of Clove (Syzygium aromaticum L.) and Clues to Its Anti-COVID-19 Utility

The current COronaVIrus Disease 19 (COVID-19) pandemic caused by SARS-CoV-2 infection is enormously affecting the worldwide health and economy. In the wait for an effective global immunization, the development of a specific therapeutic protocol to treat COVID-19 patients is clearly necessary as a short-term solution of the problem. Drug repurposing and herbal medicine represent two of the most explored strategies for an anti-COVID-19 drug discovery. Clove (Syzygium aromaticum L.) is a well-known culinary spice that has been used for centuries in folk medicine in many disorders. Interestingly, traditional medicines have used clove since ancient times to treat respiratory ailments, whilst clove ingredients show antiviral and anti-inflammatory properties. Other interesting features are the clove antithrombotic, immunostimulatory, and antibacterial effects. Thus, in this review, we discuss the potential role of clove in the frame of anti-COVID-19 therapy, focusing on the antiviral, anti-inflammatory, and antithrombotic effects of clove and its molecular constituents described in the scientific literature.

Identification and characterization of circRNAs encoded by MERS-CoV, SARS-CoV-1 and SARS-CoV-2

The life-threatening coronaviruses MERS-CoV, SARS-CoV-1 and SARS-CoV-2 (SARS-CoV-1/2) have caused and will continue to cause enormous morbidity and mortality to humans. Virus-encoded noncoding RNAs are poorly understood in coronaviruses. Data mining of viral-infection-related RNA-sequencing data has resulted in the identification of 28 754, 720 and 3437 circRNAs encoded by MERS-CoV, SARS-CoV-1 and SARS-CoV-2, respectively. MERS-CoV exhibits much more prominent ability to encode circRNAs in all genomic regions than those of SARS-CoV-1/2. Viral circRNAs typically exhibit low expression levels. Moreover, majority of the viral circRNAs exhibit expressions only in the late stage of viral infection. Analysis of the competitive interactions of viral circRNAs, human miRNAs and mRNAs in MERS-CoV infections reveals that viral circRNAs up-regulated genes related to mRNA splicing and processing in the early stage of viral infection, and regulated genes involved in diverse functions including cancer, metabolism, autophagy, viral infection in the late stage of viral infection. Similar analysis in SARS-CoV-2 infections reveals that its viral circRNAs down-regulated genes associated with metabolic processes of cholesterol, alcohol, fatty acid and up-regulated genes associated with cellular responses to oxidative stress in the late stage of viral infection. A few genes regulated by viral circRNAs from both MERS-CoV and SARS-CoV-2 were enriched in several biological processes such as response to reactive oxygen and centrosome localization. This study provides the first glimpse into viral circRNAs in three deadly coronaviruses and would serve as a valuable resource for further studies of circRNAs in coronaviruses.

Immunity, virus evolution, and effectiveness of SARS-CoV-2 vaccines

Phylogenetic and pathogenesis studies of the severe acute respiratory syndrome-related coronaviruses (SARS-CoVs) strains have highlighted some specific mutations that could confer the RNA genome fitness advantages and immunological resistance for their rapid spread in the human population. The analyses of 30 kb RNA SARS-CoVs genome sequences, protein structures, and functions have provided us a perspective of how host-virus protein-protein complexes act to mediate virus infection. The open reading frame (ORF)1a and ORF1b translation yields 16 non-structural (nsp1-16) and 6 accessory proteins (p6, p7a, p8ab, p9b) with multiple functional domains. Viral proteins recruit over 300 host partners forming hetero-oligomeric complexes enabling the viral RNA synthesis, packing, and virion release. Many cellular host factors and the innate immune cells through pattern-recognition receptors and intracellular RNA sensor molecules act to inhibit virus entry and intracellular replication. However, non-structural ORF proteins hijack them and suppress interferon synthesis and its antiviral effects. Pro-inflammatory chemokines and cytokines storm leads to dysfunctional inflammation, lung injury, and several clinical symptoms in patients. During the global pandemic, COVID-19 patients were identified with non-synonymous substitution of G614D in the spike protein, indicating virus co-evolution in host cells. We review findings that suggest that host RNA editing and DNA repair systems, while carrying on recombination, mutation, and repair of viral RNA intermediates, may facilitate virus evolution. Understanding how the host cell RNA replication process may be driven by SARS-CoV-2 RNA genome fitness will help the testing of vaccines effectiveness to multiple independent mutated coronavirus strains that will emerge.

SARS-CoV-2: Insights into its structural intricacies and functional aspects for drug and vaccine development

Globally, SARS-CoV-2 has emerged as threat to life and economy. Researchers are trying to find a cure against this pathogen but without much success. Several attempts have been made to understand the atomic level details of SARS-CoV-2 in the past few months. However, one review with all structural details for drug and vaccine development has been missing. Hence, this review aims to summarize key functional roles played by various domains of SARS-CoV-2 genome during its entry into the host, replication, repression of host immune response and overall viral life cycle. Additionally, various proteins of SARS-CoV-2 for finding a potent inhibitor have also been highlighted. To mitigate this deadly virus, an understanding of atomic level information, pathogenicity mechanisms and functions of different proteins in causing the infection is imperative. Thus, these structural details would finally pave the way for development of a potential drug/vaccine against the disease caused by SARS-CoV-2.

Nucleoside Analogs and Nucleoside Precursors as Drugs in the Fight against SARS-CoV-2 and Other Coronaviruses

Coronaviruses (CoVs) are positive-sense RNA enveloped viruses, members of the family Coronaviridae, that cause infections in a broad range of mammals including humans. Several CoV species lead to mild upper respiratory infections typically associated with common colds. However, three human CoV (HCoV) species: Severe Acute Respiratory Syndrome (SARS)-CoV-1, Middle East Respiratory Syndrome (MERS)-CoV, and SARS-CoV-2, are responsible for severe respiratory diseases at the origin of two recent epidemics (SARS and MERS), and of the current COronaVIrus Disease 19 (COVID-19), respectively. The easily transmissible SARS-CoV-2, emerging at the end of 2019 in China, spread rapidly worldwide, leading the World Health Organization (WHO) to declare COVID-19 a pandemic. While the world waits for mass vaccination, there is an urgent need for effective drugs as short-term weapons to combat the SARS-CoV-2 infection. In this context, the drug repurposing approach is a strategy able to guarantee positive results rapidly. In this regard, it is well known that several nucleoside-mimicking analogs and nucleoside precursors may inhibit the growth of viruses providing effective therapies for several viral diseases, including HCoV infections. Therefore, this review will focus on synthetic nucleosides and nucleoside precursors active against different HCoV species, paying great attention to SARS-CoV-2. This work covers progress made in anti-CoV therapy with nucleoside derivatives and provides insight into their main mechanisms of action.

Predictive Value of CAR for In-Hospital Mortality in Patients with COVID-19 Pneumonia: A Retrospective Cohort Study

Background

In the current literature, there is a growing evidence that supports the significant role of inflammation in the progression of viral pneumonia, including patients with coronavirus disease 2019 (COVID-19).

Aim

The present study aimed to investigate the predictive value of C-reactive protein/albumin ratio (CAR) for in-hospital mortality in patients with COVID-19.

Material and Methods

This retrospective study included the data of 275 consecutive COVID-19 patients who were hospitalized in a referral pandemic center. The CAR ratio was obtained by dividing the CRP level with albumin level. The study population was divided into tertiles (T1, T2, and T3) according to their admission CAR values. The endpoint of the study was a composite outcome of in-hospital mortality.

Results

During the in-hospital course, 33 (12%) patients died. The patients classified into T3 group had significantly higher CAR compared those classified into T2 and T1 groups. After the adjustment for the confounders, T3 group had 8.2 (95% CI: 4.2–48.1) times higher rates of in-hospital mortality compared to T1 group (the reference group) in a logistic regression model using CAR values.

Conclusion

To the best of our knowledge, this is the first study to demonstrate the predictive value of CAR for in-hospital mortality in COVID-19 patients.

Effect of human umbilical cord-derived mesenchymal stem cells on lung damage in severe COVID-19 patients: a randomized, double-blind, placebo-controlled phase 2 trial

Treatment of severe Coronavirus Disease 2019 (COVID-19) is challenging. We performed a phase 2 trial to assess the efficacy and safety of human umbilical cord-mesenchymal stem cells (UC-MSCs) to treat severe COVID-19 patients with lung damage, based on our phase 1 data. In this randomized, double-blind, and placebo-controlled trial, we recruited 101 severe COVID-19 patients with lung damage. They were randomly assigned at a 2:1 ratio to receive either UC-MSCs (4 × 107 cells per infusion) or placebo on day 0, 3, and 6. The primary endpoint was an altered proportion of whole lung lesion volumes from baseline to day 28. Other imaging outcomes, 6-minute walk test (6-MWT), maximum vital capacity, diffusing capacity, and adverse events were recorded and analyzed. In all, 100 COVID-19 patients were finally received either UC-MSCs (n = 65) or placebo (n = 35). UC-MSCs administration exerted numerical improvement in whole lung lesion volume from baseline to day 28 compared with the placebo (the median difference was -13.31%, 95% CI -29.14%, 2.13%, P = 0.080). UC-MSCs significantly reduced the proportions of solid component lesion volume compared with the placebo (median difference: -15.45%; 95% CI -30.82%, -0.39%; P = 0.043). The 6-MWT showed an increased distance in patients treated with UC-MSCs (difference: 27.00 m; 95% CI 0.00, 57.00; P = 0.057). The incidence of adverse events was similar in the two groups. These results suggest that UC-MSCs treatment is a safe and potentially effective therapeutic approach for COVID-19 patients with lung damage. A phase 3 trial is required to evaluate effects on reducing mortality and preventing long-term pulmonary disability. (Funded by The National Key R&D Program of China and others. ClinicalTrials.gov number, NCT04288102.

Brilacidin Demonstrates Inhibition of SARS-CoV-2 in Cell Culture

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the newly emergent causative agent of coronavirus disease-19 (COVID-19), has resulted in more than two million deaths worldwide since it was first detected in 2019. There is a critical global need for therapeutic intervention strategies that can be deployed to safely treat COVID-19 disease and reduce associated morbidity and mortality. Increasing evidence shows that both natural and synthetic antimicrobial peptides (AMPs), also referred to as Host Defense Proteins/Peptides (HDPs), can inhibit SARS-CoV-2, paving the way for the potential clinical use of these molecules as therapeutic options. In this manuscript, we describe the potent antiviral activity exerted by brilacidin-a de novo designed synthetic small molecule that captures the biological properties of HDPs-on SARS-CoV-2 in a human lung cell line (Calu-3) and a monkey cell line (Vero). These data suggest that SARS-CoV-2 inhibition in these cell culture models is likely to be a result of the impact of brilacidin on viral entry and its disruption of viral integrity. Brilacidin demonstrated synergistic antiviral activity when combined with remdesivir. Collectively, our data demonstrate that brilacidin exerts potent inhibition of SARS-CoV-2 against different strains of the virus in cell culture.

Factual insights of the allosteric inhibition mechanism of SARS-CoV-2 main protease by quercetin: an in silico analysis

SARS-CoV-2 main protease (Mpro) cleaves the viral polypeptide 1a and 1ab in a site-specific ((L-Q|(S, A, G)) manner and produce functional enzymes for mediating viral replication. Numerous studies have reported synthetic competitive inhibitors against this target enzyme but increase in substrate concentration often reduces the effectiveness of such inhibitors. Allosteric inhibition by natural compound can provide safe and effective treatment by alleviating this limitation. Present study deals with in silico allosteric inhibition analysis of quercetin, against SARS-CoV-2-Mpro. Molecular docking of quercetin with Mpro revealed consistent binding of quercetin at a site other than active site in multiple runs, with the highest binding energy of - 8.31 kcal/mol, forming 6 H-bonds with residues Gln127, Cys128, Lys137, Asp289 and Glu290. Molecular dynamic simulation of 50 ns revealed high stability of Mpro-quercetin complex with RMSD values ranging from 0.1 to 0.25 nm. Moreover, native-Mpro and Mpro-quercetin complex conformations extracted at different time points from simulation trajectories were subjected to active site-specific docking with modelled substrate peptide (AVLQSGFR) by ZDOCK server. Results displayed site-specific cleavage of peptide when docked with native-Mpro. While substrate peptide remained intact when docked with Mpro-quercetin complex, also the binding energy of peptide reduced from 785 to 86 from 1 to 50 ns as quercetin induced alterations in the active site cavity reducing its affinity for the substrate. Further, no interactions were noticed between peptide and active site residues of Mpro-quercetin complex conformations at 40 and 50 ns. Hence, quercetin displayed effective allosteric inhibition potential against SARS-CoV-2 Mpro, and can be developed into an efficient treatment for COVID-19.

Non-linear correlation between daily new cases of COVID-19 and meteorological factors in 127 countries

Meteorological parameters are the critical factors of affecting respiratory infectious disease such as Middle East Respiratory Syndrome (MERS), Severe Acute Respiratory Syndrome (SARS) and influenza, however, the effect of meteorological parameters on coronavirus disease 2019 (COVID-19) remains controversial. This study investigated the effects of meteorological factors on daily new cases of COVID-19 in 127 countries, as of August 31 2020. The log-linear generalized additive model (GAM) was used to analyze the effect of meteorological variables on daily new cases of COVID-19. Our findings revealed that temperature, relative humidity, and wind speed are nonlinearly correlated with daily new cases, and they may be negatively correlated with the daily new cases of COVID-19 over 127 countries when temperature, relative humidity and wind speed were below 20°C, 70% and 7 m/s respectively. Temperature(>20°C) was positively correlated with daily new cases. Wind speed (when>7 m/s) and relative humidity (>70%) was not statistically associated with transmission of COVID-19. The results of this research will be a useful supplement to help healthcare policymakers in the Belt and Road countries, the Centers for Disease Control (CDC) and the World Health Organization (WHO) to develop strategies to combat COVID-19.

An overview of chitosan and its application in infectious diseases

Infectious diseases, such as the coronavirus disease-19, SARS virus, Ebola virus, and AIDS, threaten the health of human beings globally. New viruses, drug-resistant bacteria, and fungi continue to challenge the human efficacious drug bank. Researchers have developed a variety of new antiviral and antibacterial drugs in response to the infectious disease crisis. Meanwhile, the development of functional materials has also improved therapeutic outcomes. As a natural material, chitosan possesses good biocompatibility, bioactivity, and biosafety. It has been proven that the cooperation between chitosan and traditional medicine greatly improves the ability of anti-infection. This review summarized the application and design considerations of chitosan-composed systems for the treatment of infectious diseases, looking forward to providing the idea of infectious disease therapy.

Interaction of small molecules with the SARS-CoV-2 papain-like protease: In silico studies and in vitro validation of protease activity inhibition using an enzymatic inhibition assay

The SARS-CoV-2 virus is causing COVID-19, an ongoing pandemic, with extraordinary global health, social, and political implications. Currently, extensive research and development efforts are aimed at producing a safe and effective vaccine. In the interim, small molecules are being widely investigated for antiviral effects. With respect to viral replication, the papain-like (PL^pro) and main proteases (M^pro), are critical for processing viral replicase polypeptides. Further, the PL^pro possesses deubiquitinating activity affecting key signalling pathways, including inhibition of interferon and innate immune antagonism. Therefore, inhibition of PL^pro activity with small molecules is an important research direction. Our aim was to focus on identification of potential inhibitors of the protease activity of SARS-CoV-2 PL^pro. We investigated 300 small compounds derived predominantly from our OliveNet™ library (222 phenolics) and supplemented with synthetic and dietary compounds with reported antiviral activities. An initial docking screen, using the potent and selective noncovalent PL^pro inhibitor, GRL-0617 as a control, enabled a selection of 30 compounds for further analyses. From further in silico analyses, including docking to scenes derived from a publicly available molecular dynamics simulation trajectory (100 μs PDB 6WX4; DESRES-ANTON-11441075), we identified lead compounds for further in vitro evaluation using an enzymatic inhibition assay measuring SARS-CoV-2 PL^pro protease activity. Our findings indicate that hypericin possessed inhibition activity, and both rutin and cyanidin-3-O-glucoside resulted in a concentration-dependent inhibition of the PL^pro, with activity in the micromolar range. Overall, hypericin, rutin, and cyanidin-3-O-glucoside can be considered lead compounds requiring further characterisation for potential antiviral effects in appropriate model systems.

Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion

Orf8, one of the most puzzling genes in the SARS lineage of coronaviruses, marks a unique and striking difference in genome organization between SARS-CoV-2 and SARS-CoV-1. Here, using sequence comparisons, we unequivocally reveal the distant sequence similarities between SARS-CoV-2 Orf8 with its SARS-CoV-1 counterparts and the X4-like genes of coronaviruses, including its highly divergent "paralog" gene Orf7a, whose product is a potential immune antagonist of known structure. Supervised sequence space walks unravel identity levels that drop below 10% and yet exhibit subtle conservation patterns in this novel superfamily, characterized by an immunoglobulin-like beta sandwich topology. We document the high accuracy of the sequence space walk process in detail and characterize the subgroups of the superfamily in sequence space by systematic annotation of gene and taxon groups. While SARS-CoV-1 Orf7a and Orf8 genes are most similar to bat virus sequences, their SARS-CoV-2 counterparts are closer to pangolin virus homologs, reflecting the fine structure of conservation patterns within the SARS-CoV-2 genomes. The divergence between Orf7a and Orf8 is exceptionally idiosyncratic, since Orf7a is more constrained, whereas Orf8 is subject to rampant change, a peculiar feature that may be related to hitherto-unknown viral infection strategies. Despite their common origin, the Orf7a and Orf8 protein families exhibit different modes of evolutionary trajectories within the coronavirus lineage, which might be partly attributable to their complex interactions with the mammalian host cell, reflected by a multitude of functional associations of Orf8 in SARS-CoV-2 compared to a very small number of interactions discovered for Orf7a.IMPORTANCE Orf8 is one of the most puzzling genes in the SARS lineage of coronaviruses, including SARS-CoV-2. Using sophisticated sequence comparisons, we confirm its origins from Orf7a, another gene in the lineage that appears as more conserved, compared to Orf8. Orf7a is a potential immune antagonist of known structure, while a deletion of Orf8 was shown to decrease the severity of the infection in a cohort study. The subtle sequence similarities imply that Orf8 has the same immunoglobulin-like fold as Orf7a, confirmed by structure determination. We characterize the subgroups of this superfamily and demonstrate the highly idiosyncratic divergence patterns during the evolution of the virus.

Integrating Metamaterial Antenna Node and LiFi for Privacy Preserving Intelligent COVID-19 Hospital Patient Management

Light fidelity (LiFi) and wireless fidelity (WiFi) can be applied with the same network under the different constraints, which is suitable for COVID-19 surveillance in hospitals. The LiFi network is a high-capacity and security platform. A COVID-19 surveillance system using LiFi is proposed, which consists of two switching modes: communication and surveillance. Firstly, the communication targets are to accommodate the electromagnetic interference (EMI) immunity and high-capacity and security data transmission, where secondly the COVID-19 surveillance can be applied. In operation, the up and downlink system uses a metamaterial antenna embedded by Mach Zehnder interferometer (MZI). An antenna consists of silver bars embedded at the microring center with two-phase modulators at its sides. The entangled source namely a dark soliton is applied to form the transmission, where the information security based on quantum cryptography can be managed. By using the suitable parameters, the whispering gallery modes (WGMs) are generated and the up and downlink nodes are formed. The input information is multiplexed with time to form the multiplexed signals, where the big data transmission (40 Pbit s - 1 ) can be employed. By using the surveillance mode, the plasmonic antenna can be applied for temperature and electric force sensors, which can offer the disinfectant spray and temperature sensor for COVID-19 applications. The optimum plasma force sensitivity is 0.16 N kg-1 mW-1. The center frequencies of 191.48 THz and 199.41 THz are obtained for uplink and downlink antennas, respectively. The optimum temperature sensitivity is 0.05 rads-1 °C-1. In conclusion, the novelty of proposed work is that the integrated sensor circuits are employed for COVID-19 surveillance in the hospital. The fuzzy-based system is designed for critical patient monitoring alert using this surveillance and management inside the hospital for COVID-19 patients.

The role of kallikrein-kinin and renin-angiotensin systems in COVID-19 infection

In November 2019 the first cases of a novel acute respiratory syndrome has been reported in Wuhan province, China. Soon after, in January 2020 the World Health Organization declared a pandemic state due to the dissemination of a virus named SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the cause of coronavirus disease 2019 (COVID-19). Being an unknown disease, it is essential to assess not only its main characteristic features and overall clinical symptomatology but also its patient infection mode and propagation to design appropriate clinical interventions and treatments. In this review the pathophysiology of SARS-CoV-2 infection and how the virus enters the cells and activates the immune system are described. The role of three systems involved in the SARS- CoV-2 infection (renin-angiotensin, kinin and coagulation systems) is discussed with the objectives to identify and try to explain several of the events observed during the evolution of the disease and to suggest possible targets for therapeutic interventions.

Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection induces dysregulation of immunity: in silico gene expression analysis

Highly pathogenic coronaviruses (CoVs) induce acute respiratory distress syndrome, and the severe acute respiratory syndrome coronavirus (SARS-CoV)-2 has caused a pandemic since late 2019. The diversity of clinical manifestations after SARS-CoV-2 infection results in great challenges to diagnose CoV disease 2019 (COVID-19). There is a growing body of published research on this topic; however, effective medications are still undergoing a long process of being assessed. In the search for potential genetic targets for this infection, we applied a holistic bioinformatics approach to study alterations of gene signatures between SARS-CoV-2-infected cells and mock-infected controls. Two different kinds of lung epithelial cells, A549 with angiotensin-converting enzyme 2 (ACE2) overexpression and normal human bronchial epithelial (NHBE) cells, were infected with SARS-CoV-2. We performed bioinformatics analyses of RNA-sequencing in this study. Through a Venn diagram, Database for Annotation, Visualization and Integrated Discovery, Gene Ontology, Ingenuity Pathway Analysis, and Gene Set Enrichment Analysis, the pathways and networks were constructed from commonly upregulated genes in SARS-CoV-2-infected lung epithelial cells. Genes associated with immune-related pathways, responses of host cells after intracellular infection, steroid hormone biosynthesis, receptor signaling, and the complement system were enriched. Dysregulation of the immune system and malfunction of interferon contribute to a failure to kill SARS-CoV-2 and exacerbate respiratory distress in severely ill patients. Current findings from this study provide a comprehensive investigation of SARS-CoV-2 infection using high-throughput technology.

COVID-19 drug repurposing: A review of computational screening methods, clinical trials, and protein interaction assays

The situation of coronavirus disease 2019 (COVID-19) pandemic is rapidly evolving, and medical researchers around the globe are dedicated to finding cures for the disease. Drug repurposing, as an efficient way for drug development, has received a lot of attention. However, the huge amount of studies makes it challenging to keep up to date with the literature on COVID-19 therapeutic development. This review addresses this challenge by grouping the COVID-19 drug repurposing research into three large groups, including clinical trials, computational research, and in vitro protein-binding experiments. Particularly, to facilitate future drug discovery and the creation of effective drug combinations, drugs are organized by their mechanisms of action and reviewed by their efficacy measured by clinical trials. Providing this subtyping information, we hope this review would serve the scientists, clinicians, and the pharmaceutical industry who are looking at the new therapeutics for COVID-19 treatment.

Design of Multi-Epitope Vaccine against SARS-CoV-2

The ongoing COVID-19 pandemic requires urgently specific therapeutics and approved vaccines. Here, the four structural proteins of the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), the causative agent of COVID-19, are screened by in-house immunoinformatic tools to identify peptides acting as potential T-cell epitopes. In order to act as an epitope, the peptide should be processed in the host cell and presented on the cell surface in a complex with the Human Leukocyte Antigen (HLA). The aim of the study is to predict the binding affinities of all peptides originating from the structural proteins of SARS-CoV-2 to 30 most frequent in the human population HLA proteins of class I and class II and to select the high binders (IC50 < 50 nM). The predicted high binders are compared to known high binders from SARS-CoV conserved in CoV-2 and 77% of them coincided. The high binders will be uploaded onto lipid nanoparticles and the multi-epitope vaccine prototype will be tested for ability to provoke T-cell mediated immunity and protection against SARS-CoV-2.

Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures

The SARS-CoV-2 pandemic, and the likelihood of future coronavirus pandemics, has rendered our understanding of coronavirus biology more essential than ever. Small molecule chemical probes offer to both reveal novel aspects of virus replication and to serve as leads for antiviral therapeutic development. The RNA-biased amiloride scaffold was recently tuned to target a viral RNA structure critical for translation in enterovirus 71, ultimately uncovering a novel mechanism to modulate positive-sense RNA viral translation and replication. Analysis of CoV RNA genomes reveal many conserved RNA structures in the 5'-UTR and proximal region critical for viral translation and replication, including several containing bulge-like secondary structures suitable for small molecule targeting. Following phylogenetic conservation analysis of this region, we screened an amiloride-based small molecule library against a less virulent human coronavirus, OC43, to identify lead ligands. Amilorides inhibited OC43 replication as seen in viral plaque assays. Select amilorides also potently inhibited replication competent SARS-CoV-2 as evident in the decreased levels of cell free virions in cell culture supernatants of treated cells. Reporter screens confirmed the importance of RNA structures in the 5'-end of the viral genome for small molecule activity. Finally, NMR chemical shift perturbation studies of the first six stem loops of the 5'-end revealed specific amiloride interactions with stem loops 4, 5a, and 6, all of which contain bulge like structures and were predicted to be strongly bound by the lead amilorides in retrospective docking studies. Taken together, the use of multiple orthogonal approaches allowed us to identify the first small molecules aimed at targeting RNA structures within the 5'-UTR and proximal region of the CoV genome. These molecules will serve as chemical probes to further understand CoV RNA biology and can pave the way for the development of specific CoV RNA-targeted antivirals.

Review a brief history of coronaviruses in Thailand

As with many countries around the world, Thailand is currently experiencing restrictions to daily life as a consequence of the worldwide transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 is the third respiratory syndrome coronavirus to be introduced into Thailand, following previous importation of cases of the severe acute respiratory syndrome coronavirus (SARS) and the Middle East respiratory syndrome coronavirus (MERS). Unlike SARS and MERS, SARS-CoV-2 was able to establish local transmission in Thailand. In addition to the imported coronaviruses, Thailand has a number of endemic coronaviruses that can affect livestock and pet species, can be found in bats, as well as four human coronaviruses that are mostly associated with the common cold. This article seeks to review what is known on both the endemic and imported coronaviruses in Thailand.

COVID-19 and cancer: From basic mechanisms to vaccine development using nanotechnology

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Shows updated understanding of SARS-CoV-2, including the interaction between ACE 2 and the viral spike protein.

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More effective vaccines are required for immunocompromised cancer patients.

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Cancer alters the immune system through different levels of D-Dimer, albumin, prothrombin, and neutrophils.

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Nanomaterials assist vaccine delivery, including viral vector and mRNA vaccines with lipid nanoparticles.

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global pandemic which has induced unprecedented ramifications, severely affecting our society due to the long incubation time, unpredictably high prevalence and lack of effective vaccines. One of the interesting notions is that there is an association between COVID-19 and cancer. Cancer patients seem to exhibit exacerbated conditions and a higher mortality rate when exposed to the virus. Therefore, vaccines are the promising solution to minimise the problem amongst cancer patients threatened by the new viral strains. However, there are still limitations to be considered, including the efficacy of COVID vaccines for immunocompromised individuals, possible interactions between the vaccine and cancer, and personalised medicine. Not only to eradicate the pandemic, but also to make it more effective for immunocompromised patients who are suffering from cancer, a successful vaccine platform is required through the implementation of nanotechnology which can also enable scalable manufacturing and worldwide distribution along with its faster and precise delivery. In this review, we summarise the current understanding of COVID-19 with clinical perspectives, highlighting the association between COVID-19 and cancer, followed by a vaccine development for this association using nanotechnology. We suggest different administration methods for the COVID-19 vaccine formulation options. This study will contribute to paving the way towards the prevention and treatment of COVID-19, especially for the immunocompromised individuals.

What is holding back the development of antiviral metallodrugs? A literature overview and implications for SARS-CoV-2 therapeutics and future viral outbreaks

In light of the Covid-19 outbreak, this review brings together historical and current literature efforts towards the development of antiviral metallodrugs. Classical compounds such as CTC-96 and auranofin are discussed in depth, as pillars for future metallodrug development. From the recent literature, both cell-based results and biophysical assays against potential viral biomolecule targets are summarized here. The comprehension of the biomolecular targets and their interactions with coordination compounds are emphasized as fundamental strategies that will foment further development of metal-based antivirals. We also discuss other possible and unexplored methods for unveiling metallodrug interactions with biomolecules related to viral replication and highlight the specific challenges involved in the development of antiviral metallodrugs.

High prevalence of pre-existing serological cross-reactivity against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in sub-Saharan Africa

Objective

Significant morbidity and mortality have occurred in the USA, Europe, and Asia due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), whereas the numbers of infections and deaths in sub-Saharan Africa (SSA) have remained comparatively low. It has been hypothesized that exposure of the population in SSA to other coronaviruses prior to the COVID-19 pandemic resulted in some degree of cross-protection against SARS-CoV-2 infection and pathogenesis. We evaluated this hypothesis by comparing SARS-CoV-2 cross-reactive antibodies in pre-pandemic plasma samples collected from SSA and the USA.

Method

Pre-COVID-19 pandemic plasma samples from SSA and the USA were collected and tested by immunofluorescence assay against the spike and nucleocapsid proteins of all known human coronaviruses (HCoVs).

Results

The prevalence of SARS-CoV-2 serological cross-reactivity was significantly higher in samples from SSA compared with the USA. Most of these cross-reactive samples cross-recognized the SARS-CoV-2 nucleocapsid protein and the spike proteins of other HCoVs. Nucleocapsid proteins from HCoV-NL63 and HCoV-229E were detected in most samples, thereby implicating prior exposure to these two HCoVs as the likely source of cross-reactive antibodies against SARS-CoV-2.

Conclusion

The low incidences of SARS-CoV-2 infection and disease in SSA appear to be correlated with the pre-pandemic serological cross-recognition of HCoVs, which are substantially more prevalent in SSA than the USA.

The Impacts of Antivirals on the Coronavirus Genome Structure and Subsequent Pathogenicity, Virus Fitness and Antiviral Design

With the global threat of SARS-CoV-2, much effort has been focused on treatment and disease control. However, how coronaviruses react to the treatments and whether the surviving viruses have altered their characteristics are also unanswered questions with medical importance. To this end, bovine coronavirus (BCoV), which is in the same genus as SARS-CoV-2, was used as a test model and the findings were as follows. With the treatment of antiviral remdesivir, the selected BCoV variant with an altered genome structure developed resistance, but its pathogenicity was not increased in comparison to that of wild type (wt) BCoV. Under the selection pressure of innate immunity, the genome structure was also altered; however, neither resistance developed nor pathogenicity increased for the selected BCoV variant. Furthermore, both selected BCoV variants showed a better efficiency in adapting to alternative host cells than wt BCoV. In addition, the previously unidentified feature that the spike protein was a common target for mutations under different antiviral treatments might pose a problem for vaccine development because spike protein is a common target for antibody and vaccine designs. The findings derived from this fundamental research may contribute to the disease control and treatments against coronaviruses, including SARS-CoV-2.

Human umbilical cord-derived mesenchymal stem cell therapy in patients with COVID-19: a phase 1 clinical trial

No effective drug treatments are available for coronavirus disease 2019 (COVID-19). Host-directed therapies targeting the underlying aberrant immune responses leading to pulmonary tissue damage, death, or long-term functional disability in survivors require clinical evaluation. We performed a parallel assigned controlled, non-randomized, phase 1 clinical trial to evaluate the safety of human umbilical cord-derived mesenchymal stem cells (UC-MSCs) infusions in the treatment of patients with moderate and severe COVID-19 pulmonary disease. The study enrolled 18 hospitalized patients with COVID-19 (n = 9 for each group). The treatment group received three cycles of intravenous infusion of UC-MSCs (3 × 10⁷ cells per infusion) on days 0, 3, and 6. Both groups received standard COVID-treatment regimens. Adverse events, duration of clinical symptoms, laboratory parameters, length of hospitalization, serial chest computed tomography (CT) images, the PaO₂/FiO₂ ratio, dynamics of cytokines, and IgG and IgM anti-SARS-CoV-2 antibodies were analyzed. No serious UC-MSCs infusion-associated adverse events were observed. Two patients receiving UC-MSCs developed transient facial flushing and fever, and one patient developed transient hypoxia at 12 h post UC-MSCs transfusion. Mechanical ventilation was required in one patient in the treatment group compared with four in the control group. All patients recovered and were discharged. Our data show that intravenous UC-MSCs infusion in patients with moderate and severe COVID-19 is safe and well tolerated. Phase 2/3 randomized, controlled, double-blinded trials with long-term follow-up are needed to evaluate the therapeutic use of UC-MSCs to reduce deaths and improve long-term treatment outcomes in patients with serious COVID-19.

SARS-CoV-2 meta-interactome suggests disease-specific, autoimmune pathophysiologies and therapeutic targets

Background: Severe coronavirus disease 2019 (COVID-19) is associated with multiple comorbidities and is characterized by an auto-aggressive inflammatory state leading to massive collateral damage. To identify preventive and therapeutic strategies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), it is important to ascertain the molecular interactions between virus and host, and how they translate into disease pathophysiology. Methods: We matched virus-human protein interactions of human coronaviruses and other respiratory viruses with lists of genes associated with autoimmune diseases and comorbidities associated to worse COVID-19 course. We then selected the genes included in the statistically significant intersection between SARS-CoV-2 network and disease associated gene sets, identifying a meta-interactome. We analyzed the meta-interactome genes expression in samples derived from lungs of infected humans, and their regulation by IFN-β. Finally, we performed a drug repurposing screening to target the network's most critical nodes. Results: We found a significant enrichment of SARS-CoV-2 interactors in immunological pathways and a strong association with autoimmunity and three prognostically relevant conditions (type 2 diabetes, coronary artery diseases, asthma), that present more independent physiopathological subnetworks. We observed a reduced expression of meta-interactome genes in human lungs after SARS-CoV-2 infection, and a regulatory potential of type I interferons. We also underscored multiple repurposable drugs to tailor the therapeutic strategies. Conclusions: Our data underscored a plausible genetic background that may contribute to the distinct observed pathophysiologies of severe COVID-19. Also, these results may help identify the most promising therapeutic targets and treatments for this condition.

Plants Metabolites: Possibility of Natural Therapeutics Against the COVID-19 Pandemic

COVID-19, a disease induced by SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2), has been the cause of a worldwide pandemic. Though extensive research works have been reported in recent days on the development of effective therapeutics against this global health crisis, there is still no approved therapy against SARS-CoV-2. In the present study, plant-synthesized secondary metabolites (PSMs) have been prioritized to make a review focusing on the efficacy of plant-originated therapeutics for the treatment of COVID-19. Plant metabolites are a source of countless medicinal compounds, while the diversity of multidimensional chemical structures has made them superior to treat serious diseases. Some have already been reported as promising alternative medicines and lead compounds for drug repurposing and discovery. The versatility of secondary metabolites may provide novel antibiotics to tackle MDR (Multi-Drug Resistant) microbes too. This review attempted to find out plant metabolites that have the therapeutic potential to treat a wide range of viral pathogens. The study includes the search of remedies belonging to plant families, susceptible viral candidates, antiviral assays, and the mode of therapeutic action; this attempt resulted in the collection of an enormous number of natural therapeutics that might be suggested for the treatment of COVID-19. About 219 plants from 83 families were found to have antiviral activity. Among them, 149 plants from 71 families were screened for the identification of the major plant secondary metabolites (PSMs) that might be effective for this pandemic. Our investigation revealed that the proposed plant metabolites can serve as potential anti- SARS-CoV-2 lead molecules for further optimization and drug development processes to combat COVID-19 and future pandemics caused by viruses. This review will stimulate further analysis by the scientific community and boost antiviral plant-based research followed by novel drug designing.

Novel Coronavirus: A Newly Arranged Mini-Review

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which was originally known as a virus that infects animals and rarely can be transmitted to humans in large populations, is now transformed into one of the most feared pandemics causes worldwide. Infection by a virus that is officially known as COVID-19 has caused global concern mainly due to the number of deaths caused. Since it was first reported in Wuhan, China in December 2019, now COVID-19 has spread to almost all parts of the world with a very rapid spread rate. The main symptom of this infection is a respiratory disease accompanied by other symptoms that resemble flu-like illness. Everyone can suffer from COVID-19, but the elderly, toddlers, pregnant women, and people with certain diseases and disorders of the immune system show more severe symptoms. The disease is transmitted through inhalation or contact with droplets, where the incubation period ranges from 2 to 14 days. Until now, specific therapy to treat COVID-19 has not been found, with preventive measures taken to control its spread. In this mini-review, we will explain important information related to COVID-19.