Coronaviruses and SARS-COV-2

Nanoarchitectonics for synergistic activity of multimetallic nanohybrids as a possible approach for antimicrobial resistance (AMR)

The global threat posed by antimicrobial resistance (AMR) to public health is an immensurable problem. The effectiveness of treating infections would be more at risk in the absence of effective antimicrobials. Researchers have shown an amplified interest in alternatives, such as developing advanced metallic nanohybrids as new therapeutic candidates for antibiotics due to their promising effectiveness against resistant microorganisms. In recent decades, the antimicrobial activity of monometallic nanoparticles has received extensive study and solid proof, providing new opportunities for developing multimetallic nanohybrid antimicrobials. Advanced metallic nanohybrids are an emerging remedy for a number of issues that develop in the field of medicine. Advanced metallic nanohybrids have shown a promising ability to combat resistant microorganisms due to their overall synergistic activity. Formulating advanced multimetallic nanohybrids falling under the umbrella of the growing field of nanoarchitectonics, which extends beyond nanotechnology. The underlying theory of nanoarchitectonics involves utilizing nanoscale units that follow the concepts of nanotechnology to architect nanomaterials. This review focuses on a comprehensive description of antimicrobial mechanisms of metallic nanohybrids and their enabling future insights on the research directions of developing the nanoarchitectonics of advanced multimetallic nanohybrids as novel antibiotics through their synergistic activity.

Development of multiplex real-time PCR for simultaneous detection of SARS-CoV-2, CCoV, and FIPV

Introduction

Coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), canine coronavirus (CCoV), and feline infectious peritonitis virus (FIPV), have the potential for interspecies transmission. These viruses can be present in complex environments where humans, dogs, and cats coexist, posing a significant threat to both human and animal safety.

Methods and results

In this study, we developed a novel multiplex TaqMan-probe-based real-time PCR assay for the simultaneous detection and differentiation of SARS-CoV-2, CCoV, and FIPV. Specific primers and TaqMan fluorescent probes were designed based on the N region of SARS-CoV-2 and FIPV, as well as the S region of CCoV, which demonstrated a remarkable sensitivity and specificity toward the targeted viruses, as few as 21.83, 17.25 and 9.25 copies/μL for SARS-CoV-2, CCoV and FIPV, respectively. The standard curve constructed by the optimized method in our present study showed a high amplification efficiency within or near the optimal range of 91% to 116% and R(2) values were at least 0.95 for the abovementioned coronaviruses. A total of 91 samples, including six plasmid mixed mock samples, four virus fluid mixing simulated samples, and 81 clinical samples, were analyzed using this method. Results demonstrated strong agreement with conventional approaches.

Discussion

By enabling the simultaneous detection of three viruses, this method enhances testing efficiency while decreasing costs. Importantly, it provides a valuable tool for the prevalence and geographical distribution of suspected and co-infected animals, ultimately contributing to the advancement of both animal and public health.

Unveiling the Multifaceted Capabilities of Endophytic Aspergillus flavus Isolated from Annona squamosa Fruit Peels against Staphylococcus Isolates and HCoV 229E-In Vitro and In Silico Investigations

Recently, there has been a surge towards searching for primitive treatment strategies to discover novel therapeutic approaches against multi-drug-resistant pathogens. Endophytes are considered unexplored yet perpetual sources of several secondary metabolites with therapeutic significance. This study aims to isolate and identify the endophytic fungi from Annona squamosa L. fruit peels using morphological, microscopical, and transcribed spacer (ITS-rDNA) sequence analysis; extract the fungus's secondary metabolites by ethyl acetate; investigate the chemical profile using UPLC/MS; and evaluate the potential antibacterial, antibiofilm, and antiviral activities. An endophytic fungus was isolated and identified as Aspergillus flavus L. from the fruit peels. The UPLC/MS revealed seven compounds with various chemical classes. The antimicrobial activity of the fungal ethyl acetate extract (FEA) was investigated against different Gram-positive and Gram-negative standard strains, in addition to resistant clinical isolates using the agar diffusion method. The CPE-inhibition assay was used to identify the potential antiviral activity of the crude fungal extract against low pathogenic human coronavirus (HCoV 229E). Selective Gram-positive antibacterial and antibiofilm activities were evident, demonstrating pronounced efficacy against both methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-sensitive Staphylococcus aureus (MSSA). However, the extract exhibited very weak activity against Gram-negative bacterial strains. The ethyl acetate extract of Aspergillus flavus L exhibited an interesting antiviral activity with a half maximal inhibitory concentration (IC50) value of 27.2 µg/mL against HCoV 229E. Furthermore, in silico virtual molecular docking-coupled dynamics simulation highlighted the promising affinity of the identified metabolite, orienting towards three MRSA biotargets and HCoV 229E main protease as compared to reported reference inhibitors/substrates. Finally, ADME analysis was conducted to evaluate the potential oral bioavailability of the identified metabolites.

Identification of potential antiviral compounds from Egyptian sea stars against MERS-CoV with the in vitro and in silico experiments

Recently, the world faced many epidemics which were caused by viral respiratory pathogens. Marine creatures including Asteroidea class have been one of the recent research topics due to their diverse and complex secondary metabolites. Some of these constituents exhibit antiviral activities. The present study aimed to extract and identify the potential antiviral compounds from Pentaceraster cumingi, Astropecten polyacanthus and Pentaceraster mammillatus. The results showed that promising activity of the methanolic extract of P. cumingi with 50% inhibitory concentration (IC50) of 3.21 mg/ml against MERS-CoV with a selective index (SI) of 13.975. The biochemical components of the extracts were identified by GC/MS analysis. The Molecular docking study highlighted the virtual mechanism of binding the identified compounds towards three PDB codes of MERS-CoV non-structural protein 10/16. Interestingly, 2-mono Linolein showed promising binding energy of -14.75 Kcal/mol with the second PDB code (5YNI) and -15.22 Kcal/mol with the third PDB code (5YNQ).

Quantitative Assessment of Energetic Contributions of Residues in a SARS-CoV-2 Viral Enzyme/Nanobody Interface

The highly conserved protease enzyme from SARS-CoV-2 (MPro) is crucial for viral replication and is an attractive target for the design of novel inhibitory compounds. MPro is known to be conformationally flexible and has been stabilized in an extended conformation in a complex with a novel nanobody (NB2B4), which inhibits the dimerization of the enzyme via binding to an allosteric site. However, the energetic contributions of the nanobody residues stabilizing the MPro/nanobody interface remain unresolved. We probed these residues using all-atom MD simulations in combination with alchemical free energy calculations by studying the physical residue-residue interactions and discovered the role of hydrophobic and electrostatic interactions in stabilizing the complex. Specifically, we found via mutational analysis that three interfacial nanobody residues (Y59, R106, and L109) contributed significantly, two residues (L107 and P110) contributed moderately, and two residues (H112 and T113) contributed minimally to the overall binding affinity of the nanobody. We also discovered that the nanobody affinity could be enhanced via a charge-reversal mutation (D62R) that alters the local interfacial electrostatic environment of this residue in the complex. These findings are potentially useful in designing novel synthetic nanobodies as allosteric inhibitors of MPro.

Was the COVID-19 epidemic synchronous in space? An analysis in the health regions of the Rio de Janeiro state, 2020-2022

OBJECTIVE

To analyze the spatio-temporal dynamics of COVID-19 in the Rio de Janeiro state within the nine health regions, between March 2020 and December 2022.

METHODS

The Poisson model with random effects was used to smooth and estimate the incidence of COVID-19 hospitalizations reported in the Influenza Epidemiological Surveillance Information System (SIVEP-Gripe) to verify the synchronicity of the epidemic in the state.

RESULTS

The COVID-19 epidemic in the state is characterized by the presence of seven peaks during the analyzed period corresponding to seven found. An asynchrony in hospitalizations was identified, varying according to the different virus variants in the nine health regions of the state. The incidence peaks of hospitalizations ranged from 1 to 12 cases per 100,000 inhabitants during the pandemic.

CONCLUSION

This spatio-temporal analysis is applicable to other scenarios, enabling monitoring and decision-making for the control of epidemic diseases in different areas.

Inhibitory Activity of Flavonoid Scaffolds on SARS-CoV-2 3CLpro: Insights from the Computational and Experimental Investigations

The emergence of the COVID-19 situation has become a global issue due to the lack of effective antiviral drugs for treatment. Flavonoids are a class of plant secondary metabolites that have antiviral activity against SARS-CoV-2 through inhibition of the main protease (3CLpro). In this study, 22 flavonoids obtained from natural sources and semisynthetic approaches were investigated for their inhibitory activity against SARS-CoV-2 3CLpro, along with cytotoxicity on Vero cells. The protein-ligand interactions were examined using molecular dynamics simulation. Moreover, QSAR analysis was conducted to clarify the structural effects on bioactivity. Accordingly, the in vitro investigation demonstrated that four flavonoids, namely, tectochrysin (7), 6″,6″-dimethylchromeno-[2″,3″:7,8]-flavone (9), panduratin A (19), and genistein (20), showed higher protease inhibitory activity compared to the standard flavonoid baicalein. Finally, our finding suggests that genistein (20), an isoflavone discovered in Millettia brandisiana, has potential for further development as a SARS-CoV-2 3CLpro inhibitor.

Porcine delta coronavirus inhibits NHE3 activity of porcine intestinal epithelial cells through miR-361-3p/NHE3 regulatory axis

Porcine deltacoronavirus (PDCoV) infection in piglets can cause small intestinal epithelial necrosis and atrophic enteritis, which leads to severe damages to host cells, and result in diarrhea. In this study, we investigated the relationship between miR-361, SLC9A3(Solute carrier family 9, subfamily A, member 3), and NHE3(sodium-hydrogen exchanger member 3) in in porcine intestinal epithelial cells (IPI-2I) cells after PDCoV infection. Our results showed that the ssc-miR-361-3p expression inhibits the mRNA level of SLC9A3 gene which lead to the descending of NHE3 protein expression, and the NHE3 activity was suppressed. NHE3 activity was suppressed via down-regulation expression of SLC9A3 mRNA by transfection with siRNA. Ssc-miR-361-3p mimics and inhibitors were used to change the expression of ssc-miR-361-3p in IPI-2I cells. Ssc-miR-361-3p overexpression reduced the mRNA level of SLC9A3 gene, the level of NHE3 protein expression and NHE3 activity in IPI-2I cells, while ssc-miR-361-3p inhibits NHE3. Furthermore, luciferase reporter assay showed that SLC9A3 gene was a direct target of ssc-miR-361-3p. Ssc-miR-361-3p inhibition restored NHE3 activity in PDCoV infected IPI-2I cells by up-regulating SLC9A3 mRNA expression and NHE3 protein expression. These results demonstrate that the PDCoV infection can inhibit NHE3 activity through miR-361-3p/SLC9A3 regulatory axis. The relevant research is reported for the first time in PDCoV, which has significance in exploring the pathogenic mechanism of PDCoV and can provide a theoretical basis for its prevention and control. suggesting that NHE3 and ssc-miR-361-3p may be potential therapeutic targets for diarrhea in infected piglets.

Structural basis for the mechanism of interaction of SARS-CoV-2 B.1.640.2 variant RBD with the host receptors hACE2 and GRP78

The inflicted chaos instigated by the SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) globally continues with the emergence of novel variants. The current global outbreak is aggravated by the manifestation of novel variants, which affect the effectiveness of the vaccine, attachment with hACE2 (human Angiotensin-converting enzyme 2) and immune evasion. Recently, a new variant named University Hospital Institute (IHU) (B.1.640.2) was reported in France in November 2021 and is spreading globally affecting public healthcare. The B.1.640.2 SARS-CoV-2 strain revealed 14 mutations and 9 deletions in spike protein. Thus, it is important to understand how these variations in the spike protein impact the communication with the host. A protein coupling approach along with molecular simulation protocols was used to interpret the variation in the binding of the wild type (WT) and B.1.640.2 variant with hACE2 and Glucose-regulating protein 78 (GRP78) receptors. The initial docking scores revealed a stronger binding of the B.1.640.2-RBD with both the hACE2 and GRP78. To further understand the crucial dynamic changes, we looked at the structural and dynamic characteristics and also explored the variations in the bonding networks between the WT and B.1.640.2-RBD (receptor-binding domain) in association with hACE2 and GRP78, respectively. Our findings revealed that the variant complex demonstrated distinct dynamic properties in contrast to the wild type due to the acquired mutations. Finally, to provide conclusive evidence on the higher binding by the B.1.640.2 variant the TBE was computed for each complex. For the WT with hACE2 the TBE was quantified to be-61.38 ± 0.96 kcal/mol and for B.1.640.2 variant the TBE was estimated to be -70.47 ± 1.00 kcal/mol. For the WT-RBD-GRP78 the TBE -was computed to be 32.32 ± 0.56 kcal/mol and for the B.1.640.2-RBD a TBE of -50.39 ± 0.88 kcal/mol was reported. This show that these mutations are the basis for higher binding and infectivity produced by B.1.640.2 variant and can be targeted for drug designing against it.Communicated by Ramaswamy H. Sarma.

Evolutionary deletions within the SARS-CoV-2 genome as signature trends for virus fitness and adaptation

Coronaviruses are large RNA viruses that can infect and spread among humans and animals. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for coronavirus disease 2019, has evolved since its first detection in December 2019. Deletions are a common occurrence in SARS-CoV-2 evolution, particularly in specific genomic sites, and may be associated with the emergence of highly competent lineages. While deletions typically have a negative impact on viral fitness, some persist and become fixed in viral populations, indicating that they may confer advantageous benefits for the virus's adaptive evolution. This work presents a literature review and data analysis on structural losses in the SARS-CoV-2 genome and the potential relevance of specific signatures for enhanced viral fitness and spread.

Regulation and functions of the NLRP3 inflammasome in RNA virus infection

Virus infection is one of the greatest threats to human life and health. In response to viral infection, the host's innate immune system triggers an antiviral immune response mostly mediated by inflammatory processes. Among the many pathways involved, the nucleotide-binding oligomerization domain (NOD)-like receptor protein 3 (NLRP3) inflammasome has received wide attention in the context of viral infection. The NLRP3 inflammasome is an intracellular sensor composed of three components, including the innate immune receptor NLRP3, adaptor apoptosis-associated speck-like protein containing CARD (ASC), and the cysteine protease caspase-1. After being assembled, the NLRP3 inflammasome can trigger caspase-1 to induce gasdermin D (GSDMD)-dependent pyroptosis, promoting the maturation and secretion of proinflammatory cytokines such as interleukin-1 (IL-1β) and interleukin-18 (IL-18). Recent studies have revealed that a variety of viruses activate or inhibit the NLRP3 inflammasome via viral particles, proteins, and nucleic acids. In this review, we present a variety of regulatory mechanisms and functions of the NLRP3 inflammasome upon RNA viral infection and demonstrate multiple therapeutic strategies that target the NLRP3 inflammasome for anti-inflammatory effects in viral infection.

The diverse roles of peroxisomes in the interplay between viruses and mammalian cells

Peroxisomes are ubiquitous organelles found in eukaryotic cells that play a critical role in the oxidative metabolism of lipids and detoxification of reactive oxygen species (ROS). Recently, the role of peroxisomes in viral infections has been extensively studied. Although several studies have reported that peroxisomes exert antiviral activity, evidence indicates that viruses have also evolved diverse strategies to evade peroxisomal antiviral signals. In this review, we summarize the multiple roles of peroxisomes in the interplay between viruses and mammalian cells. Focus is given on the peroxisomal regulation of innate immune response, lipid metabolism, ROS production, and viral regulation of peroxisomal biosynthesis and degradation. Understanding the interactions between peroxisomes and viruses provides novel insights for the development of new antiviral strategies.

Impact of the lockdown period during the COVID-19 pandemic on the metal content of the anemone Anemonia sulcata in the Canary Islands (CE Atlantic, Spain)

Anemones, specifically the species Anemonia sulcata, are cnidarians that serve as bioindicators in marine ecosystems, indicating the health of the environment and changes in environmental conditions. Monitoring anemone populations and studying their well-being and distribution provide valuable insights into marine ecosystem conditions. This study aimed to investigate the impact of the SARS-CoV-2 pandemic on the metal content of Anemonia sulcata. Over a six-year period (2017-2022), twenty specimens of Anemonia sulcata were collected in Tenerife, Spain. The results showed that in 2020, during the two-month lockdown in Spain from March to May when tourism was halted, A. sulcata exhibited the lowest concentrations of various metals studied (Al, Cd, Cu, Fe, Pb, and Zn). This finding suggests that the reduced anthropogenic pressure on the coast due to the absence of tourism significantly decreased pollution levels. Therefore, the study emphasizes the importance of promoting sustainable tourism worldwide. The research highlights that minimizing human impact on coastal areas through responsible tourism practices can effectively reduce pollution in marine ecosystems.

Engineering Proteins for Cell Entry

Proteins are essential for life, as they participate in all vital processes in the body. In the past decade, delivery of active proteins to specific cells and organs has attracted increasing interest. However, most proteins cannot enter the cytoplasm due to the cell membrane acting as a natural barrier. To overcome this challenge, various proteins have been engineered to acquire cell-penetrating capacity by mimicking or modifying natural shuttling proteins. In this review, we provide an overview of the different types of engineered cell-penetrating proteins such as cell-penetrating peptides, supercharged proteins, receptor-binding proteins, and bacterial toxins. We also discuss some strategies for improving endosomal escape such as pore formation, the proton sponge effect, and hijacking intracellular trafficking pathways. Finally, we introduce some novel methods and technologies for designing and detecting engineered cell-penetrating proteins.

Inhibition of SARS-CoV-2 Infection in Vero Cells by Bovine Lactoferrin under Different Iron-Saturation States

Despite the rapid mass vaccination against COVID-19, the emergence of new SARS-CoV-2 variants of concern, such as omicron, is still a great distress, and new therapeutic options are needed. Bovine lactoferrin (bLf), a multifunctional iron-binding glycoprotein available in unsaturated (apo-bLf) and saturated (holo-bLf) forms, has been shown to exert broad-spectrum antiviral activity against many viruses. In this study, we evaluated the efficacy of both forms of bLf at 1 mg/mL against infection of Vero cells by SARS-CoV-2. As assessed with antiviral assays, an equivalent significant reduction in virus infection by about 70% was observed when either form of bLf was present throughout the infection procedure with the SARS-CoV-2 ancestral or omicron strain. This inhibitory effect seemed to be concentrated during the early steps of virus infection, since a significant reduction in its efficiency by about 60% was observed when apo- or holo-bLf were incubated with the cells before or during virus addition, with no significant difference between the antiviral effects of the distinct iron-saturation states of the protein. However, an ultrastructural analysis of bLf treatment during the early steps of virus infection revealed that holo-bLf was somewhat more effective than apo-bLf in inhibiting virus entry. Together, these data suggest that bLf mainly acts in the early events of SARS-CoV-2 infection and is effective against the ancestral virus as well as its omicron variant. Considering that there are no effective treatments to COVID-19 with tolerable toxicity yet, bLf shows up as a promising candidate.

Highly-specific aptamer targeting SARS-CoV-2 S1 protein screened on an automatic integrated microfluidic system for COVID-19 diagnosis

Variants of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) have evolved such that it may be challenging for diagnosis and clinical treatment of the pandemic coronavirus disease-19 (COVID-19). Compared with developed SARS-CoV-2 diagnostic tools recently, aptamers may exhibit some advantages, including high specificity/affinity, longer shelf life (vs. antibodies), and could be easily prepared. Herein an integrated microfluidic system was developed to automatically carry out one novel screening process based on the systematic evolution of ligands by exponential enrichment (SELEX) for screening aptamers specific with SARS-CoV-2. The new screening process started with five rounds of positive selection (with the S1 protein of SARS-CoV-2). In addition, including non-target viruses (influenza A and B), human respiratory tract-related cancer cells (adenocarcinoma human alveolar basal epithelial cells and dysplastic oral keratinocytes), and upper respiratory tract-related infectious bacteria (including methicillin-resistant Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae), and human saliva were involved to increase the specificity of the screened aptamer during the negative selection. Totally, all 10 rounds could be completed within 20 h. The dissociation constant of the selected aptamer was determined to be 63.0 nM with S1 protein. Limits of detection for Wuhan and Omicron clinical strains were found to be satisfactory for clinical applications (i.e. 4.80 × 10¹ and 1.95 × 10² copies/mL, respectively). Moreover, the developed aptamer was verified to be capable of capturing inactivated SARS-CoV-2 viruses, eight SARS-CoV-2 pseudo-viruses, and clinical isolates of SARS-CoV-2 viruses. For high-variable emerging viruses, this developed integrated microfluidic system can be used to rapidly select highly-specific aptamers based on the novel SELEX methods to deal with infectious diseases in the future.

HDAC-Specific Inhibitors Induce the Release of Porcine Epidemic Diarrhea Virus via the COPII-Coated Vesicles

Porcine epidemic diarrhea virus (PEDV) is an alpha-coronavirus causing acute diarrhea and high mortality in neonatal suckling piglets, resulting in huge economic losses for the global swine industry. The replication, assembly and cell egression of PEDV, an enveloped RNA virus, are mediated via altered intracellular trafficking. The underlying mechanisms of PEDV secretion are poorly understood. In this study, we found that the histone deacetylase (HDAC)-specific inhibitors, trichostatin A (TSA) and sodium butyrate (NaB), facilitate the secretion of infectious PEDV particles without interfering with its assembly. We found that PEDV N protein and its replicative intermediate dsRNA colocalize with coat protein complex II (COPII)-coated vesicles. We also showed that the colocalization of PEDV and COPII is enhanced by the HDAC-specific inhibitors. In addition, ultrastructural analysis revealed that the HDAC-specific inhibitors promote COPII-coated vesicles carrying PEDV virions and the secretion of COPII-coated vesicles. Consistently, HDAC-specific inhibitors-induced PEDV particle secretion was abolished by Sec24B knockdown, implying that the HDAC-specific inhibitors-mediated COPII-coated vesicles are required for PEDV secretion. Taken together, our findings provide initial evidence suggesting that PEDV virions can assemble in the endoplasmic reticulum (ER) and bud off from the ER in the COPII-coated vesicles. HDAC-specific inhibitors promote PEDV release by hijacking the COPII-coated vesicles.

SARS-CoV-2 neutralising antibody therapies: Recent advances and future challenges

The COVID-19 pandemic represents an unparalleled global public health crisis. Despite concerted research endeavours, the repertoire of effective treatment options remains limited. However, neutralising-antibody-based therapies hold promise across an array of practices, encompassing the prophylaxis and management of acute infectious diseases. Presently, numerous investigations into COVID-19-neutralising antibodies are underway around the world, with some studies reaching clinical application stages. The advent of COVID-19-neutralising antibodies signifies the dawn of an innovative and promising strategy for treatment against SARS-CoV-2 variants. Comprehensively, our objective is to amalgamate contemporary understanding concerning antibodies targeting various regions, including receptor-binding domain (RBD), non-RBD, host cell targets, and cross-neutralising antibodies. Furthermore, we critically examine the prevailing scientific literature supporting neutralising antibody-based interventions, and also delve into the functional evaluation of antibodies, with a particular focus on in vitro (vivo) assays. Lastly, we identify and consider several pertinent challenges inherent to the realm of COVID-19-neutralising antibody-based treatments, offering insights into potential future directions for research and development.

The Use of Quantitative Electroencephalography (QEEG) to Assess Post-COVID-19 Concentration Disorders in Professional Pilots: An Initial Concept

Announced by WHO in 2020, the global COVID-19 pandemic caused by SARS-CoV-2 has affected many people, leading to serious health consequences. These consequences are observed in the daily lives of infected patients as various dysfunctions and limitations. More and more people are suffering post-COVID-19 complications that interfere with or completely prevent them from working or even functioning independently on a daily basis. The aim of our study was to demonstrate that innovative quantitative electroencephalography (QEEG) can be used to assess cognitive function disorders reported after the COVID-19 pandemic. It is worth noting that no similar study has been conducted to date in a group of pilots. The QEEG method we used is currently one of the basic neurological examinations, enabling easy observation of post-COVID-19 changes in the nervous system. With the innovativeness of this technique, our study shows that the use of quantitative electroencephalography can be a precursor in identifying complications associated with cognitive function disorders after COVID-19. Our study was conducted on twelve 26-year-old pilots. All participants had attended the same flight academy and had contracted SARS-CoV-2 infection. The pilots began to suspect COVID-19 infection when they developed typical symptoms such as loss of smell and taste, respiratory problems, and rapid fatigue. Quantitative electroencephalography (QEEG), which is one of the most innovative forms of diagnostics, was used to diagnose the patients. Comparison of the results between the study and control groups showed significantly higher values of all measurements of alpha, theta, and beta2 waves in the study group. In the case of the sensorimotor rhythm (SMR), the measurement results were significantly higher in the control group compared to the study group. Our study, conducted on pilots who had recovered from COVID-19, showed changes in the amplitudes of brain waves associated with relaxation and concentration. The results confirmed the issues reported by pilots as evidenced by the increased amplitudes of alfa, theta, and beta2 waves. It should be emphasized that the modern diagnostic method (QEEG) presented here has significant importance in the medical diagnosis of various symptoms and observation of treatment effects in individuals who have contracted the SARS-CoV-2 virus. The present study demonstrated an innovative approach to the diagnosis of neurological complications after COVID-19.

Nano-Enabled Antivirals for Overcoming Antibody Escaped Mutations Based SARS-CoV-2 Waves

This review discusses receptor-binding domain (RBD) mutations related to the emergence of various SARS-CoV-2 variants, which have been highlighted as a major cause of repetitive clinical waves of COVID-19. Our perusal of the literature reveals that most variants were able to escape neutralizing antibodies developed after immunization or natural exposure, pointing to the need for a sustainable technological solution to overcome this crisis. This review, therefore, focuses on nanotechnology and the development of antiviral nanomaterials with physical antagonistic features of viral replication checkpoints as such a solution. Our detailed discussion of SARS-CoV-2 replication and pathogenesis highlights four distinct checkpoints, the S protein (ACE2 receptor coupling), the RBD motif (ACE2 receptor coupling), ACE2 coupling, and the S protein cleavage site, as targets for the development of nano-enabled solutions that, for example, prevent viral attachment and fusion with the host cell by either blocking viral RBD/spike proteins or cellular ACE2 receptors. As proof of this concept, we highlight applications of several nanomaterials, such as metal and metal oxide nanoparticles, carbon-based nanoparticles, carbon nanotubes, fullerene, carbon dots, quantum dots, polymeric nanoparticles, lipid-based, polymer-based, lipid-polymer hybrid-based, surface-modified nanoparticles that have already been employed to control viral infections. These nanoparticles were developed to inhibit receptor-mediated host-virus attachments and cell fusion, the uncoating of the virus, viral gene expression, protein synthesis, the assembly of progeny viral particles, and the release of the virion. Moreover, nanomaterials have been used as antiviral drug carriers and vaccines, and nano-enabled sensors have already been shown to enable fast, sensitive, and label-free real-time diagnosis of viral infections. Nano-biosensors could, therefore, also be useful in the remote testing and tracking of patients, while nanocarriers probed with target tissue could facilitate the targeted delivery of antiviral drugs to infected cells, tissues, organs, or systems while avoiding unwanted exposure of non-target tissues. Antiviral nanoparticles can also be applied to sanitizers, clothing, facemasks, and other personal protective equipment to minimize horizontal spread. We believe that the nanotechnology-enabled solutions described in this review will enable us to control repeated SAR-CoV-2 waves caused by antibody escape mutations.

A Potential Association between Ribonuclease 1 Dynamics in the Blood and the Outcome in COVID-19 Patients

The COVID-19 pandemic caused by the new SARS-CoV-2 coronavirus is the most recent and well-known outbreak of a coronavirus. RNase 1 is a small endogenous antimicrobial polypeptide that possesses antiviral activity against viral diseases. In this study, we investigated a potential association between ribonuclease 1 and the outcome in COVID-19 patients and the impact of increased and decreased RNase 1 levels serum during the course of the disease. Therefore, two patient populations, Cohort A (n = 35) and B (n = 80), were subclassified into two groups, in which the RNase 1 concentration increased or decreased from time point one to time point two. We show that the RNase 1 serum levels significantly increased in the increasing group of both cohorts (p = 0.0171; p < 0.0001). We detect that patients in the increasing group who died had significantly higher RNase 1 serum levels at both time points in Cohort A (p = 0.0170; p = 0.0393) and Cohort B (p = 0.0253; p = 0.0034) than patients who survived. Additionally, we measured a significant correlation of RNase 1 serum levels with serum creatinine as well as creatinine clearance in the increasing and decreasing group at both time points of Cohort A. Based on these results, there is now good evidence that RNase 1 may play a role in renal dysfunction associated with ICU COVID-19 patients and that increasing RNase 1 serum level may be a potential biomarker to predict outcome in COVID-19 patients.

Severe Acute Respiratory Syndrome Associated Infections

Viral infections are some of the most common sources of respiratory illness in pediatric and adult populations worldwide. Influenza and coronaviruses are viral pathogens that could lead to severe respiratory illness and death. More recently, respiratory illness from coronaviruses, accounts for more than 1 million deaths in the United States alone. This article will explore the epidemiology, pathogenesis, diagnosis, treatment, and prevention of severe acute respiratory syndrome caused by coronavirus-2, and Middle Eastern respiratory syndrome.

Ensemble Deep Learning Derived from Transfer Learning for Classification of COVID-19 Patients on Hybrid Deep-Learning-Based Lung Segmentation: A Data Augmentation and Balancing Framework

BACKGROUND AND MOTIVATION

Lung computed tomography (CT) techniques are high-resolution and are well adopted in the intensive care unit (ICU) for COVID-19 disease control classification. Most artificial intelligence (AI) systems do not undergo generalization and are typically overfitted. Such trained AI systems are not practical for clinical settings and therefore do not give accurate results when executed on unseen data sets. We hypothesize that ensemble deep learning (EDL) is superior to deep transfer learning (TL) in both non-augmented and augmented frameworks.

METHODOLOGY

The system consists of a cascade of quality control, ResNet-UNet-based hybrid deep learning for lung segmentation, and seven models using TL-based classification followed by five types of EDL's. To prove our hypothesis, five different kinds of data combinations (DC) were designed using a combination of two multicenter cohorts-Croatia (80 COVID) and Italy (72 COVID and 30 controls)-leading to 12,000 CT slices. As part of generalization, the system was tested on unseen data and statistically tested for reliability/stability.

RESULTS

Using the K5 (80:20) cross-validation protocol on the balanced and augmented dataset, the five DC datasets improved TL mean accuracy by 3.32%, 6.56%, 12.96%, 47.1%, and 2.78%, respectively. The five EDL systems showed improvements in accuracy of 2.12%, 5.78%, 6.72%, 32.05%, and 2.40%, thus validating our hypothesis. All statistical tests proved positive for reliability and stability.

CONCLUSION

EDL showed superior performance to TL systems for both (a) unbalanced and unaugmented and (b) balanced and augmented datasets for both (i) seen and (ii) unseen paradigms, validating both our hypotheses.

Serological screening of SARS-CoV-2 infection in companion animals of Buenos Aires suburbs

The Coronavirus Disease 2019 (COVID-19) is a zoonotic disease caused by the pandemic virus SARS-CoV-2. Domestic and wild animals are susceptible to infection and are potential reservoirs for virus variants. To date, there is no information about the exposure of companion animals in Buenos Aires Suburbs, the area with the largest population in Argentina where the highest number of COVID-19 human cases occurred during the first infection wave. Here we developed a multi-species indirect ELISA to measure antibodies reactive to the SARS-CoV-2 receptor-binding domain (RBD) from several vertebrates constituting the class Mammalia, making it a valuable tool for field serosurveillance. The ELISA cut-off value was estimated by sera from dogs, cats, cattle, and pigs sampled before 2019 (n = 170), considering a 98% percentile and a grey zone to completely exclude any false positive result. Specificity was confirmed by measuring levels of neutralizing antibodies against canine coronavirus, the avidity of specific antibodies, and their capacity to impede the binding of a recombinant RBD protein to VERO cells in an In-Cell ELISA. Sera from 464 cats and dogs sampled in 2020 and 2021 ("pandemic" samples) were assessed using the RBD-ELISA. Information on COVID-19 disease in the household and the animals' lifestyles was collected. In Buenos Aires Suburbs cats were infected at a higher proportion than dogs, seroprevalence was 7.1 and 1.68%, respectively. Confirmed COVID-19 in the caregivers and outdoor lifestyle were statistically associated with seropositivity in cats. The risk of cats getting infected living indoors in COVID-19-negative households was null. The susceptibility of mammals to SARS-CoV-2, the possibility of transmission between animals themselves and humans, together with the free-roaming lifestyle typical of Buenos Aires suburban companion animals, urge pursuing responsible animal care and avoiding human interaction with animals during the disease course. The multi-species RBD-ELISA we developed can be used as a tool for serosurveillance of SARS-CoV-2 infection in mammalians (domestic and wild), guiding further targeted virological analyses to encounter susceptible species, interspecies transmission, and potential virus reservoirs in our region.

Vessel-on-a-Chip: A Powerful Tool for Investigating Endothelial COVID-19 Fingerprints

Coronavirus disease (COVID-19) causes various vascular and blood-related reactions, including exacerbated responses. The role of endothelial cells in this acute response is remarkable and may remain important beyond the acute phase. As we move into a post-COVID-19 era (where most people have been or will be infected by the SARS-CoV-2 virus), it is crucial to define the vascular consequences of COVID-19, including the long-term effects on the cardiovascular system. Research is needed to determine whether chronic endothelial dysfunction following COVID-19 could lead to an increased risk of cardiovascular and thrombotic events. Endothelial dysfunction could also serve as a diagnostic and therapeutic target for post-COVID-19. This review covers these topics and examines the potential of emerging vessel-on-a-chip technology to address these needs. Vessel-on-a-chip would allow for the study of COVID-19 pathophysiology in endothelial cells, including the analysis of SARS-CoV-2 interactions with endothelial function, leukocyte recruitment, and platelet activation. "Personalization" could be implemented in the models through induced pluripotent stem cells, patient-specific characteristics, or genetic modified cells. Adaptation for massive testing under standardized protocols is now possible, so the chips could be incorporated for the personalized follow-up of the disease or its sequalae (long COVID) and for the research of new drugs against COVID-19.

Understanding the Relationship of the Human Bacteriome with COVID-19 Severity and Recovery

The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) first emerged in 2019 in China and has resulted in millions of human morbidities and mortalities across the globe. Evidence has been provided that this novel virus originated in animals, mutated, and made the cross-species jump to humans. At the time of this communication, the Coronavirus disease (COVID-19) may be on its way to an endemic form; however, the threat of the virus is more for susceptible (older and immunocompromised) people. The human body has millions of bacterial cells that influence health and disease. As a consequence, the bacteriomes in the human body substantially influence human health and disease. The bacteriomes in the body and the immune system seem to be in constant association during bacterial and viral infections. In this review, we identify various bacterial spp. In major bacteriomes (oral, nasal, lung, and gut) of the body in healthy humans and compare them with dysbiotic bacteriomes of COVID-19 patients. We try to identify key bacterial spp. That have a positive effect on the functionality of the immune system and human health. These select bacterial spp. Could be used as potential probiotics to counter or prevent COVID-19 infections. In addition, we try to identify key metabolites produced by probiotic bacterial spp. That could have potential anti-viral effects against SARS-CoV-2. These metabolites could be subject to future therapeutic trials to determine their anti-viral efficacies.

Epidemiology, clinical characteristics and risk factors of coronavirus disease 2019 (COVID-19) in Casablanca

This is an analytical cross-sectional study of coronavirus disease 2019 (COVID-19) based on data collected between 1 November 2020 and 31 March 2021 in Casablanca focusing on the disease's epidemiological status and risk factors. A total of 4569 samples were collected and analysed by reverse-transcription polymerase chain reaction (RT-PCR); 967 patients were positive, representing a prevalence of 21.2 % for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The mean age was 47.5±18 years, and infection was more common in young adults (<60 years). However, all age groups were at risk of COVID-19, and in terms of disease severity, the elderly were at greater risk because of potential underlying health problems. Among the clinical signs reported in this study, loss of taste and/or smell, fever, cough and fatigue were highly significant predictors of a positive COVID-19 test result (P<0.001). An assessment of the reported symptoms revealed that 27 % of COVID-19-positive patients (n=261) experienced loss of taste and/or smell, whereas only 2 % (n=72) of COVID-19-negative patients did (P<0.001). This result was consistent between univariate (OR=18.125) and multivariate (adjusted OR=10.484) logistic regression analyses, indicating that loss of taste and/or smell is associated with a more than 10-fold higher multivariate adjusted probability of a positive COVID-19 test (adjusted OR=10.48; P<0.001). Binary logistic regression model analysis based on clinical signs revealed that loss of taste and/or smell had a performance index of 0.846 with a P<0.001, confirming the diagnostic utility of this symptom for the prediction of COVID-19-positive status. In conclusion, symptom evaluation and a RT-PCR [taking into account cycle threshold (C _t) values of the PCR proxy] test remain the most useful screening tools for diagnosing COVID-19. However, loss of taste/smell, fatigue, fever and cough remain the strongest independent predictors of a positive COVID-19 result.

Immune evasion of neutralizing antibodies by SARS-CoV-2 Omicron

Since its emergence at the end of 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the infection of more than 600 million people worldwide and has significant damage to global medical, economic, and political structures. Currently, a highly mutated variant of concern, SARS-CoV-2 Omicron, has evolved into many different subvariants mainly including BA.1, BA.2, BA.3, BA.4/5, and the recently emerging BA.2.75.2, BA.2.76, BA.4.6, BA.4.7, BA.5.9, BF.7, BQ.1, BQ.1.1, XBB, XBB.1, etc. Mutations in the N-terminal domain (NTD) of the spike protein, such as A67V, G142D, and N212I, alter the antigenic structure of Omicron, while mutations in the spike receptor binding domain (RBD), such as R346K, Q493R, and N501Y, increase the affinity for angiotensin-converting enzyme 2 (ACE2). Both types of mutations greatly increase the capacity of Omicron to evade immunity from neutralizing antibodies, produced by natural infection and/or vaccination. In this review, we systematically assess the immune evasion capacity of SARS-CoV-2, with an emphasis on the neutralizing antibodies generated by different vaccination regimes. Understanding the host antibody response and the evasion strategies employed by SARS-CoV-2 variants will improve our capacity to combat newly emerging Omicron variants.

Surveillance of Influenza and Other Airborne Transmission Viruses during the 2021/2022 Season in Hospitalized Subjects in Tuscany, Italy

Winter in the northern hemisphere is characterized by the circulation of influenza viruses, which cause seasonal epidemics, generally from October to April. Each influenza season has its own pattern, which differs from one year to the next in terms of the first influenza case notification, the period of highest incidence, and the predominant influenza virus subtypes. After the total absence of influenza viruses in the 2020/2021 season, cases of influenza were again recorded in the 2021/2022 season, although they remained below the seasonal average. Moreover, the co-circulation of the influenza virus and the SARS-CoV-2 pandemic virus was also reported. In the context of the DRIVE study, oropharyngeal swabs were collected from 129 Tuscan adults hospitalized for severe acute respiratory infection (SARI) and analyzed by means of real-time polymerase chain reaction (RT-PCR) for SARS-CoV-2 and 21 different airborne pathogens, including influenza viruses. In total, 55 subjects tested positive for COVID-19, 9 tested positive for influenza, and 3 tested positive for both SARS-CoV-2 and the A/H3N2 influenza virus. The co-circulation of different viruses in the population requires strengthened surveillance that is no longer restricted to the winter months. Indeed, constant, year-long monitoring of the trends of these viruses is needed, especially in at-risk groups and elderly people.

Insights on the interaction of SARS-CoV-2 variant B.1.617.2 with antibody CR3022 and analysis of antibody resistance

BACKGROUND

The existence of mutated Delta (B.1.617.2) variants of SARS-CoV-2 causes rapid transmissibility, increase in virulence, and decrease in the effectiveness of public health. Majority of mutations are seen in the surface spike, and they are considered as antigenicity and immunogenicity of the virus. Hence, finding suitable cross antibody or natural antibody and understanding its biomolecular recognition for neutralizing surface spike are crucial for developing many clinically approved COVID-19 vaccines. Here, we aim to design SARS-CoV-2 variant and hence, to understand its mechanism, binding affinity and neutralization potential with several antibodies.

RESULTS

In this study, we modelled six feasible spike protein (S1) configurations for Delta SARS-CoV-2 (B.1.617.2) and identified the best structure to interact with human antibodies. Initially, the impact of mutations at the receptor-binding domain (RBD) of B.1.617.2 was tested, and it is found that all mutations increase the stability of proteins (ΔΔG) and decrease the entropies. An exceptional case is noted for the mutation of G614D variant for which the vibration entropy change is found to be within the range of 0.133-0.004 kcal/mol/K. Temperature-dependent free energy change values (ΔG) for wild type is found to be - 0.1 kcal/mol, whereas all other cases exhibit values within the range of - 5.1 to - 5.5 kcal/mol. Mutation on spike increases the interaction with the glycoprotein antibody CR3022 and the binding affinity (CLUSpro energy =  - 99.7 kcal/mol). The docked Delta variant with the following antibodies, etesevimab, bebtelovimab, BD-368-2, imdevimab, bamlanivimab, and casirivimab, exhibit a substantially decreased docking score (- 61.7 to - 112.0 kcal/mol) and the disappearance of several hydrogen bond interactions.

CONCLUSION

Characterization of antibody resistance for Delta variant with respect to the wild type gives understanding regarding why Delta variant endures the resistance boosted through several trademark vaccines. Several interactions with CR3022 have appeared compared to Wild for Delta variant, and hence, it is suggested that modification on the CR3022 antibody could further improve for the prevention of viral spread. Antibody resistance decreased significantly due to numerous hydrogen bond interactions which clearly indicate that these marketed/launched vaccines (etesevimab) will be effective for Delta variants.

Nasal sprays for treating COVID-19: a scientific note

Clinical management of COVID-19 has been a daunting task. Due to the lack of specific treatment, vaccines have been regarded as the first line of defence. Innate responses and cell-mediated systemic immunity, including serum antibodies, have been the primary focus of practically all studies of the immune response to COVID-19. However, owing to the difficulties encountered by the conventional route, alternative routes for prophylaxis and therapy became the need of the hour. The first site invaded by SARS-CoV-2 is the upper respiratory tract. Nasal vaccines are already in different stages of development. Apart from prophylactic purposes, mucosal immunity can be exploited for therapeutic purposes too. The nasal route for drug delivery offers many advantages over the conventional route. Besides offering a needle-free delivery, they can be self-administered. They present less logistical burden as there is no need for refrigeration. The present article focuses on various aspects of nasal spray for eliminating COVID-19.

Assessment of GO-Based Protein Interaction Affinities in the Large-Scale Human–Coronavirus Family Interactome

SARS-CoV-2 is a novel coronavirus that replicates itself via interacting with the host proteins. As a result, identifying virus and host protein-protein interactions could help researchers better understand the virus disease transmission behavior and identify possible COVID-19 drugs. The International Committee on Virus Taxonomy has determined that nCoV is genetically 89% compared to the SARS-CoV epidemic in 2003. This paper focuses on assessing the host–pathogen protein interaction affinity of the coronavirus family, having 44 different variants. In light of these considerations, a GO-semantic scoring function is provided based on Gene Ontology (GO) graphs for determining the binding affinity of any two proteins at the organism level. Based on the availability of the GO annotation of the proteins, 11 viral variants, viz., SARS-CoV-2, SARS, MERS, Bat coronavirus HKU3, Bat coronavirus Rp3/2004, Bat coronavirus HKU5, Murine coronavirus, Bovine coronavirus, Rat coronavirus, Bat coronavirus HKU4, Bat coronavirus 133/2005, are considered from 44 viral variants. The fuzzy scoring function of the entire host–pathogen network has been processed with ~180 million potential interactions generated from 19,281 host proteins and around 242 viral proteins. ~4.5 million potential level one host–pathogen interactions are computed based on the estimated interaction affinity threshold. The resulting host–pathogen interactome is also validated with state-of-the-art experimental networks. The study has also been extended further toward the drug-repurposing study by analyzing the FDA-listed COVID drugs.

SARS‑CoV‑2 and Seizure: An Insight Into the Pathophysiology

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Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans

Comprehensive identification of possible target cells for viruses is crucial for understanding the pathological mechanism of virosis. The susceptibility of cells to viruses depends on many factors. Besides the existence of receptors at the cell surface, effective expression of viral genes is also pivotal for viral infection. The regulation of viral gene expression is a multilevel process including transcription, translational initiation and translational elongation. At the translational elongation level, the translational efficiency of viral mRNAs mainly depends on the match between their codon composition and cellular translational machinery (usually referred to as codon adaptation). Thus, codon adaptation for viral ORFs in different cell types may be related to their susceptibility to viruses. In this study, we selected the codon adaptation index (CAI) which is a common codon adaptation-based indicator for assessing the translational efficiency at the translational elongation level to evaluate the susceptibility to two-pandemic viruses (HIV-1 and SARS-CoV-2) of different human cell types. Compared with previous studies that evaluated the infectivity of viruses based on codon adaptation, the main advantage of our study is that our analysis is refined to the cell-type level. At first, we verified the positive correlation between CAI and translational efficiency and strengthened the rationality of our research method. Then we calculated CAI for ORFs of two viruses in various human cell types. We found that compared to high-expression endogenous genes, the CAIs of viral ORFs are relatively low. This phenomenon implied that two kinds of viruses have not been well adapted to translational regulatory machinery in human cells. Also, we indicated that presumptive susceptibility to viruses according to CAI is usually consistent with the results of experimental research. However, there are still some exceptions. Finally, we found that two viruses have different effects on cellular translational mechanisms. HIV-1 decouples CAI and translational efficiency of endogenous genes in host cells and SARS-CoV-2 exhibits increased CAI for its ORFs in infected cells. Our results implied that at least in cases of HIV-1 and SARS-CoV-2, CAI can be regarded as an auxiliary index to assess cells' susceptibility to viruses but cannot be used as the only evidence to identify viral target cells.

Design of hACE2-based small peptide inhibitors against spike protein of SARS-CoV-2: a computational approach

COVID-19 which is caused by the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has been declared pandemic in 2019. Though there is development of vaccines but there is an emergence requirement of drugs against SARS-CoV-2. Antiviral peptides can be rationally created and improved based on the known structures of viral proteins and their biological targets. In the given study, small peptide inhibitors with three amino acids are designed and docked against SARS-CoV-2 coronavirus using molecular docking approach. All the designed peptides bind at the active site but the highest binding affinity was observed for HisGluAsp. Molecular dynamics was performed to validate the stability and interactions of compound. The molecule has followed the druglikeness properties and with highest probability of being absorbed by the gastrointestinal tract. The results of the current investigation point to the possibility that the identified small peptides may prevent SARS-CoV-2 infection, although additional wet-lab tests are still required to confirm these results.

Evaluation of Clinical, Biochemical, and Demographic Characteristics of Paediatric COVID-19 Patients Admitted to Dicle University Hospital

INTRODUCTION AND AIM

In this study, we aim to determine how laboratory parameters were related to the clinical courses of patients admitted to the Dicle University Faculty of Medicine Department of Paediatrics and Paediatric Intensive Care Unit with COVID-19 diagnoses from March 2020 to November 2021.

MATERIALS AND METHOD

Clinical, biochemical and demographic characteristics of 220 patients between 0 and 16 years old with COVID-19 diagnoses at admission were analysed retrospectively.

RESULTS

We found that 57.3% of patients were male and 42.7% female, with a mean age of 107.8 ± 65.5 (range 1-192) months. Of the cases, 48.6% (n = 107) were asymptomatic, 35.5% (n = 78) were mild, 11.8% (n = 26) were moderately severe and 3.6% (n = 8) were severe. The patients' site of admission, mortality rates, C reactive protein (CRP), lactate dehydrogenase (LDH), ferritin, and fibrinogen levels differed significantly (p < 0.001).

CONCLUSION

It is important to learn about the clinical course of the disease by accurately interpreting the results of blood parameters and appropriate imaging studies.

Phytocompounds as a source for the development of new drugs to treat respiratory viral infections

Respiratory viruses have an important history as a threat to global health. However, this problem has been aggravated due to the appearance of new outbreaks caused by a newly discovered virus or variant. Recently, the new coronavirus (SARS-CoV-2) has been a major concern for health authorities, and it was classified as a pandemic by the World Health Organization. Secondary metabolites obtained from plants represent an alternative to the discovery of new active molecules and have already shown potential to combat different viruses. In an effort to demonstrate the broad spectrum of antiviral action from these metabolites, this work describes the compounds that were effective against the major viruses that cause respiratory infections in humans. In addition, their mechanisms of action were highlighted as an approach to better understanding the virus-bioactive substance relationship. Finally, this study warns that, although phytocompounds have a broad antiviral action spectrum, the development of products and clinical trials based on these secondary metabolites is still scarce and therefore deserves greater attention from the scientific community.

Flavonoids from the roots and rhizomes of Sophoratonkinensis and their in vitro anti-SARS-CoV-2 activity

Acute respiratory infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had caused a global pandemic since 2019, and posed a serious threat to global health security. Traditional Chinese medicine (TCM) has played an indispensable role in the battle against the epidemic. Many components originated from TCMs were found to inhibit the production of SARS-CoV-2 3C-like protease (3CLpro) and papain-like protease (PLpro), which are two promising therapeutic targets to inhibit SARS-CoV-2. This study describes a systematic investigation of the roots and rhizomes of Sophora tonkinensis, which results in the characterization of 12 new flavonoids, including seven prenylated flavanones (1-7), one prenylated flavonol (8), two prenylated chalcones (9-10), one isoflavanone (11), and one isoflavan dimer (12), together with 43 known compounds (13-55). Their structures including the absolute configurations were elucidated by comprehensive analysis of MS, 1D and 2D NMR data, and time-dependent density functional theory electronic circular dichroism (TDDFT ECD) calculations. Compounds 12 and 51 exhibited inhibitory effects against SARS-CoV-2 3CLpro with IC₅₀ values of 34.89 and 19.88 μmol·L^-1, repectively while compounds 9, 43 and 47 exhibited inhibitory effects against PLpro with IC₅₀ values of 32.67, 79.38, and 16.74 μmol·L^-1, respectively.

Multimodal ultrasound imaging with conventional B-mode, elastography, and parametric analysis of contrast-enhanced ultrasound (CEUS): A novel approach to assess small bowel manifestation in severe COVID-19 disease

The aim was to describe the small bowel morphology with conventional B-mode and elastography and additionally to evaluate dynamic effects of COVID-19 associated small bowel microvascularization using CEUS with color coded perfusion parameters.Thirteen patients with severe COVID-19 acute respiratory distress syndrome (ARDS) were investigated. 13 patients required intensive care treatment with mechanical ventilation. Five patients required extracorporeal membrane oxygenation (ECMO). Contrast-enhanced ultrasound (CEUS) was performed by an experienced investigator as a bolus injection of up to 2.4 ml sulfur hexafluoride microbubbles via a central venous catheter. In the parametric analysis of CEUS, the flare of microbubbles over time is visualized with colors. This is the first work using parametric analysis of CEUS to detect perfusion differences in the small bowel.Parametric analysis of CEUS in the intestinal phase was carried out, using DICOM loops for 20 seconds. In 5 patients, parametric analysis revealed intraindividual differences in contrast agent behavior in the small bowel region. Analogous to the computed tomography (CT) images parametric analysis showed regions of simultaneous hyper- and hypoperfusion of the small intestine in a subgroup of patients. In 5 patients, the parametric image of transmural global contrast enhancement was visualized.Our results using CEUS to investigate small bowel affection in COVID-19 suggest that in severe COVID-19 ARDS systemic inflammation and concomitant micro embolisms may lead to disruption of the epithelial barrier of the small intestine.This is the first study using parametric analysis of CEUS to evaluate the extent of small bowel involvement in severe COVID-19 disease and to detect microemboli. In summary, we show that in COVID-19 the small bowel may also be an important interaction site. This is in line with the fact that enterocytes have been shown to a plenitude of angiotensin converting enzyme (ACE)-2 receptors as entry sites of the virus.

All Microbiological Aspects of SARS-CoV-2 Virus

The COVID-19 disease, caused by SARS-CoV-2 virus, which was first seen in Wuhan (China) on December 31, 2019, rapidly spread to cities, countries, and continents and was noted in history as the first pandemic caused by coronaviruses. According to the World Health Organization reports, more than 645 million confirmed SARS-CoV-2-positive cases and more than 6.5 million confirmed deaths were noted all over the world during the pandemic (between December 2020 and December 2022). Although SARS-CoV-2 is a virus belonging to the coronavirus family, our knowledge of the pathogenesis and immune response of SARS-CoV-2 is still limited. Approximately 10 years (2012) after the Middle East Respiratory Syndrome (MERS-CoV) (nearly 2200 confirmed cases and 791 confirmed deaths) and 20 years (2002-2004) after the SARS-CoV epidemic (29 different countries, nearly 8000 confirmed cases, and 774 confirmed deaths), the current COVID-19 pandemic is a reminder of how new pathogens can emerge and spread rapidly, eventually causing serious public health problems. Further research is needed to establish animal models for SARSCoV-2 to investigate replication, transmission dynamics, and pathogenesis in humans in order to develop effective antiviral treatments and vaccines.

Current trends in COVID-19 diagnosis and its new variants in physiological fluids: Surface antigens, antibodies, nucleic acids, and RNA sequencing

Rapid, highly sensitive, and accurate virus circulation monitoring techniques are critical to limit the spread of the virus and reduce the social and economic burden. Therefore, point-of-use diagnostic devices have played a critical role in addressing the outbreak of COVID-19 (SARS-CoV-2) viruses. This review provides a comprehensive overview of the current techniques developed for the detection of SARS-CoV-2 in various body fluids (e.g., blood, urine, feces, saliva, tears, and semen) and considers the mutations (i.e., Alpha, Beta, Gamma, Delta, Omicron). We classify and comprehensively discuss the detection methods depending on the biomarker measured (i.e., surface antigen, antibody, and nucleic acid) and the measurement techniques such as lateral flow immunoassay (LFIA), enzyme-linked immunosorbent assay (ELISA), reverse transcriptase-polymerase chain reaction (RT-PCR), reverse transcription loop-mediated isothermal amplification (RT-LAMP), microarray analysis, clustered regularly interspaced short palindromic repeats (CRISPR) and biosensors. Finally, we addressed the challenges of rapidly identifying emerging variants, detecting the virus in the early stages of infection, the detection sensitivity, selectivity, and specificity, and commented on how these challenges can be overcome in the future.

Current strategies for SARS-CoV-2 molecular detection

The molecular detection of SARS-CoV-2 is extremely important for the discovery and prevention of pandemic dissemination. Because SARS-CoV-2 is not always present in the samples that can be collected, the sample chosen for testing has inevitably become the key to the SARS-CoV-2 positive cases screening. The nucleotide amplification strategy mainly includes Q-PCR assays and isothermal amplification assays. The Q-PCR assay is the most used SARS-CoV-2 detection assay. Due to heavy expenditures and other drawbacks, isothermal amplification cannot replace the dominant position of the Q-PCR assay. The antibody-based detection combined with Q-PCR can help to find more positive cases than only using nucleotide amplification-based assays. Pooled testing based on Q-PCR significantly increases efficiency and reduces the cost of massive-scale screening. The endless stream of variants emerging across the world poses a great challenge to SARS-CoV-2 molecular detection. The multi-target assays and several other strategies have proved to be efficient in the detection of mutated SARS-CoV-2 variants. Further research work should concentrate on: (1) identifying more ideal sample plucking strategies, (2) ameliorating the Q-PCR primer and probes targeted toward mutated SARS-CoV-2 variants, (3) exploring more economical and precise isothermal amplification assays, and (4) developing more advanced strategies for antibody/antigen or engineered antibodies to ameliorate the antibody/antigen-based strategy.

Antibacterial and Antiviral Effects of Ag, Cu and Zn Metals, Respective Nanoparticles and Filter Materials Thereof against Coronavirus SARS-CoV-2 and Influenza A Virus

Due to the high prevalence of infectious diseases and their concurrent outbreaks, there is a high interest in developing novel materials with antimicrobial properties. Antibacterial and antiviral properties of a range of metal-based nanoparticles (NPs) are a promising means to fight airborne diseases caused by viruses and bacteria. The aim of this study was to test antimicrobial metals and metal-based nanoparticles efficacy against three viruses, namely influenza A virus (H1N1; A/WSN/1933) and coronaviruses TGEV and SARS-CoV-2; and two bacteria, Escherichia coli and Staphylococcus aureus. The efficacy of ZnO, CuO, and Ag NPs and their respective metal salts, i.e., ZnSO₄, CuSO₄, and AgNO₃, was evaluated in suspensions, and the compounds with the highest antiviral efficacy were chosen for incorporation into fibers of cellulose acetate (CA), using electrospinning to produce filter materials for face masks. Among the tested compounds, CuSO₄ demonstrated the highest efficacy against influenza A virus and SARS-CoV-2 (1 h IC50 1.395 mg/L and 0.45 mg/L, respectively), followed by Zn salt and Ag salt. Therefore, Cu compounds were selected for incorporation into CA fibers to produce antiviral and antibacterial filter materials for face masks. CA fibers comprising CuSO₄ decreased SARS-CoV-2 titer by 0.38 logarithms and influenza A virus titer by 1.08 logarithms after 5 min of contact; after 1 h of contact, SARS-COV-2 virus was completely inactivated. Developed CuO- and CuSO₄-based filter materials also efficiently inactivated the bacteria Escherichia coli and Staphylococcus aureus. The metal NPs and respective metal salts were potent antibacterial and antiviral compounds that were successfully incorporated into the filter materials of face masks. New antibacterial and antiviral materials developed and characterized in this study are crucial in the context of the ongoing SARS-CoV-2 pandemic and beyond.

PSTCNN: Explainable COVID-19 diagnosis using PSO-guided self-tuning CNN

Since 2019, the coronavirus disease-19 (COVID-19) has been spreading rapidly worldwide, posing an unignorable threat to the global economy and human health. It is a disease caused by severe acute respiratory syndrome coronavirus 2, a single-stranded RNA virus of the genus Betacoronavirus. This virus is highly infectious and relies on its angiotensin-converting enzyme 2-receptor to enter cells. With the increase in the number of confirmed COVID-19 diagnoses, the difficulty of diagnosis due to the lack of global healthcare resources becomes increasingly apparent. Deep learning-based computer-aided diagnosis models with high generalisability can effectively alleviate this pressure. Hyperparameter tuning is essential in training such models and significantly impacts their final performance and training speed. However, traditional hyperparameter tuning methods are usually time-consuming and unstable. To solve this issue, we introduce Particle Swarm Optimisation to build a PSO-guided Self-Tuning Convolution Neural Network (PSTCNN), allowing the model to tune hyperparameters automatically. Therefore, the proposed approach can reduce human involvement. Also, the optimisation algorithm can select the combination of hyperparameters in a targeted manner, thus stably achieving a solution closer to the global optimum. Experimentally, the PSTCNN can obtain quite excellent results, with a sensitivity of 93.65%±1.86%, a specificity of 94.32%±2.07%, a precision of 94.30%±2.04%, an accuracy of 93.99%±1.78%, an F1-score of 93.97%±1.78%, Matthews Correlation Coefficient of 87.99%±3.56%, and Fowlkes-Mallows Index of 93.97%±1.78%. Our experiments demonstrate that compared to traditional methods, hyperparameter tuning of the model using an optimisation algorithm is faster and more effective.

The Delta and Omicron Variants of SARS-CoV-2: What We Know So Far

The world has not yet completely overcome the fear of the havoc brought by SARS-CoV-2. The virus has undergone several mutations since its initial appearance in China in December 2019. Several variations (i.e., B.1.616.1 (Kappa variant), B.1.617.2 (Delta variant), B.1.617.3, and BA.2.75 (Omicron variant)) have emerged throughout the pandemic, altering the virus's capacity to spread, risk profile, and even symptoms. Humanity faces a serious threat as long as the virus keeps adapting and changing its fundamental function to evade the immune system. The Delta variant has two escape alterations, E484Q and L452R, as well as other mutations; the most notable of these is P681R, which is expected to boost infectivity, whereas the Omicron has about 60 mutations with certain deletions and insertions. The Delta variant is 40-60% more contagious in comparison to the Alpha variant. Additionally, the AY.1 lineage, also known as the "Delta plus" variant, surfaced as a result of a mutation in the Delta variant, which was one of the causes of the life-threatening second wave of coronavirus disease 2019 (COVID-19). Nevertheless, the recent Omicron variants represent a reminder that the COVID-19 epidemic is far from ending. The wave has sparked a fervor of investigation on why the variant initially appeared to propagate so much more rapidly than the other three variants of concerns (VOCs), whether it is more threatening in those other ways, and how its type of mutations, which induce minor changes in its proteins, can wreck trouble. This review sheds light on the pathogenicity, mutations, treatments, and impact on the vaccine efficacy of the Delta and Omicron variants of SARS-CoV-2.

COVID-19 Risk Management in Dental Offices: A Review Article

BACKGROUND: As all the dental staff, including nurses and practitioners, are exposed to various routes of contamination due to the novel COVID-19 virus, which is still unknown to the scientific world, developing strategies to reduce the risk of transmission and decontaminate surfaces in a dental office would be of high importance. Although there is still insufficient data on managing this virus in dental offices, several studies have suggested protocols for improving care. AIM: This study aimed to review present investigations and reach a conclusion on what we know and need to know to combat this virus. MATERIALS AND METHODS: In this review, Scopus, PubMed, and MEDLINE databases were searched using the keywords “COVID-19,” “SARS-CoV-2,” “Medical Disinfectants,” “Personal Protective Equipment’s,” and “Surface Decontamination.” Articles were reviewed, and finally, relevant articles published during 2000–2022 were included in the final paper. RESULTS: The present research concluded that using a combination of the face shield and N95 masks protected the eyes, nose, and mouth. To have more efficient protection, water-resistant long-sleeved gowns and gloves were highly suggested. To overcome aerosols, high-performance air filters and ultraviolet were found quite effective. Allowing the patient to use antiseptic mouthwash before starting the treatment could reduce oral microorganisms and the following airborne contamination. CONCLUSION: This review has gathered all available data regarding dentistry and COVID-19 in order to conclude what has been achieved yet in the prevention of this virus through dental offices; however, more investigations are needed to have a definitive protocol against the virus.

Molecular evolution of human coronavirus-NL63, -229E, -HKU1 and -OC43 in hospitalized children in China

Human coronaviruses (HCoVs) HCoV-NL63, HCoV-229E, HCoV-HKU1 and HCoV-OC43 have been circulated in the human population worldwide, and they are associated with a broad range of respiratory diseases with varying severity. However, there are neither effective therapeutic drugs nor licensed vaccines available for the treatment and prevention of infections by the four HCoVs. In this study, we collected nasopharyngeal aspirates of children hospitalized for respiratory tract infection in China during 2014-2018 and conducted next-generation sequencing. Sequences of four HCoVs were then selected for an in-depth analysis. Genome sequences of 2 HCoV-NL63, 8 HCoV-229E, 2 HCoV-HKU1, and 6 HCoV-OC43 were obtained. Based on the full-length S gene, a strong temporal signal was found in HCoV-229E and the molecular evolutionary rate was 6 × 10^-4 substitutions/site/year. Based on the maximum-likelihood (ML) phylogenetic tree of complete S gene, we designated H78 as a new sub-genotype C2 of HCoV-HKU1, and the obtained P43 sequence was grouped into the reported novel genotype K of HCoV-OC43 circulating in Guangzhou, China. Based on the complete genome, potential recombination events were found to occur as two phenomena, namely intraspecies and interspecies. Moreover, we observed two amino acid substitutions in the S1 subunit of obtained HCoV-NL63 (G534V) and HCoV-HKU1 (H512R), while residues 534 and 512 are important for the binding of angiotensin-converting enzyme 2 and neutralizing antibodies, respectively. Our findings might provide a clue for the molecular evolution of the four HCoVs and help in the early diagnosis, treatment and prevention of broad-spectrum HCoV infection.

Muscle dysfunction in the long coronavirus disease 2019 syndrome: Pathogenesis and clinical approach

In long coronavirus disease 2019 (long COVID-19), involvement of the musculoskeletal system is characterised by the persistence or appearance of symptoms such as fatigue, muscle weakness, myalgia, and decline in physical and functional performance, even at 4 weeks after the onset of acute symptoms of COVID-19. Muscle injury biomarkers are altered during the acute phase of the disease. The cellular damage and hyperinflammatory state induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may contribute to the persistence of symptoms, hypoxaemia, mitochondrial damage, and dysregulation of the renin-angiotensin system. In addition, the occurrence of cerebrovascular diseases, involvement of the peripheral nervous system, and harmful effects of hospitalisation, such as the use of drugs, immobility, and weakness acquired in the intensive care unit, all aggravate muscle damage. Here, we review the multifactorial mechanisms of muscle tissue injury, aggravating conditions, and associated sequelae in long COVID-19.

Nanozyme and Stimulated Fluorescent Cu-Based Metal-Organic Frameworks (Cu-MOFs) Functionalized with Engineered Aptamers as a Molecular Recognition Element for Thrombin Detection in the Plasma of COVID-19 Patients

An essential tool in the management and control of the COVID-19 pandemic is the development of a fast, selective, sensitive, and inexpensive COVID-19 biomarkers detection method. Herein, an ultrasensitive and label-free biosensing strategy was described for the colorimetric and fluorimetric detection of thrombin. A dual-mode aptasensing method based on integrating engineered ssDNA with a stimulated fluorescent enzyme-mimetic copper-based metal-organic framework (Cu-MOF) as a molecular recognition element for thrombin was investigated. Cu-MOFs displayed stimulated fluorescence and enzyme-mimetic peroxidase activities that oxidize the chromogenic colorless substance TMB to blue-colored oxTMB. The thrombin-based aptamer (ssDNA) can be immobilized on the Cu-MOF surface to form a functionalized composite, ssDNA/MOF, and quench the stimulated fluorescence emission and the enzymatic activity of the Cu-MOF. Later, addition of thrombin recovers the fluorescence and enzymatic activity of the MOF. Thus, a turn-on colorimetry/fluorimetry aptasensing probe was designed for the detection of thrombin. Based on colorimetric assay, 350 pM was recorded as the lower limit of detection (LOD), while based on the fluorescence mode, 110 fM was recorded as the LOD (when S/N = 3). The label-free aptasensing probe was used successfully for the detection of thrombin in COVID-19 patients with satisfactory recoveries, 95-98%. Since the detection time of our aptasensor is relatively rapid (45 min) and due to the low-cost precursors and easy-to-operate characteristics, we believe that it has great potential to be used in point-of-care testing (POCT).

Dietary supplements for the management of COVID-19 symptoms

SARS-CoV-2, the etiological agent of COVID-19, caused a pandemic in 2020, which is only recently slowing down. The symptoms of COVID-19 range from cough to fever and pneumonia and may persist beyond the active state of the infection, in a condition called post-COVID syndrome. The aim of this paper is to review the relationship between COVID-19 and nutrition and to discuss to most up-to-date dietary supplements proposed for COVID-19 treatment and prevention. Nutrition and nutritional dysregulations, such as obesity and malnutrition, are prominent risk factors for severe COVID-19. These factors exert anti-inflammatory and proinflammatory effects on the immune system, thus exacerbating or reducing the immunological response against the virus. As for the nutritional habits, the Western diet induces a chronic inflammatory state, whereas the Mediterranean diet exerts anti-inflammatory effects and has been proposed for ameliorating COVID-19 evolution and symptoms. Several vaccines have been researched and commercialized for COVID-19 prevention, whereas several drugs, although clinically tested, have not shown promising effects. To compensate for the lack of treatment, several supplements have been recommended for preventing or ameliorating COVID-19 symptoms. Thus, it is critical to review the dietary supplements proposed for COVID-19 treatment. Supplements containing α-cyclodextrin and hydroxytyrosol exhibited promising effects in several clinical trials and reduced the severity of the outcomes and the duration of the infection. Moreover, a supplement containing hydroxytyrosol, acetyl L-carnitine, and vitamins B, C, and D improved the symptoms of patients with post-COVID syndrome.