Ultrastructural characterization of SARS coronavirus

Membrane nanotubes transform into double-membrane sheets at condensate droplets

Cellular membranes exhibit a multitude of highly curved morphologies such as buds, nanotubes, cisterna-like sheets defining the outlines of organelles. Here, we mimic cell compartmentation using an aqueous two-phase system of dextran and poly(ethylene glycol) encapsulated in giant vesicles. Upon osmotic deflation, the vesicle membrane forms nanotubes, which undergo surprising morphological transformations at the liquid-liquid interfaces inside the vesicles. At these interfaces, the nanotubes transform into cisterna-like double-membrane sheets (DMS) connected to the mother vesicle via short membrane necks. Using super-resolution (stimulated emission depletion) microscopy and theoretical considerations, we construct a morphology diagram predicting the tube-to-sheet transformation, which is driven by a decrease in the free energy. Nanotube knots can prohibit the tube-to-sheet transformation by blocking water influx into the tubes. Because both nanotubes and DMSs are frequently formed by cellular membranes, understanding the formation and transformation between these membrane morphologies provides insight into the origin and evolution of cellular organelles.

Reconstruction of the real 3D shape of the SARS-CoV-2 virus

The photographs of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus taken by electron transmission microscopy and cryoelectron microscopy provide only a 2D silhouette. The viruses appear to look like distorted circles. The present paper questions the real shape of the SARS-CoV-2 virus and makes an attempt to give an answer. Is this a general ellipsoid, a spheroid with rotational symmetry, a sphere, or something else? The answer requires the application of tools from three different disciplines: structural mechanics, microbiology, and statistics. A total of 590 virus photographs taken from 22 recently published papers were examined. From this experimental data pool, the histogram of diameter ratios was built from the 283 measurements where the virus images could be approximated as ellipses. The curve peaks at the diameter ratio of 1.22. The transformation equation for the spatial shape to the planar shade was derived for a fixed light source of the microscope. This equation involves an unknown orientation of the viruses with respect to the microscope. Two sets of models were developed, one with a uniform distribution of the virus orientation and the other with the orientation defined by the normalized beta distribution. In both sets of models, the unknown diameter ratio of the spheroidal virus was regarded as a random realization from translated gamma distributions. The parameters of the distribution of the kernel functions were determined by minimizing the mean square difference between the predicted and measured 2D histograms. The information included in the measured histograms was found to be insufficient to find an unknown distribution of the virus's orientation. Simply too many unknown parameters render the solution physically unrealistic. The minimization procedure with a uniform probability of virus orientation predicted the peak of the aspect ratio of the 3D spheroid at 1.32. Based on this result, models of the virus will be developed in the continuation of this research for a full dynamic analysis.

SARS-CoV-2 ORF3a drives dynamic dense body formation for optimal viral infectivity

SARS-CoV-2 uses the double-membrane vesicles as replication organelles. However, how virion assembly occurs has not been fully understood. Here we identified a SARS-CoV-2-driven membrane structure named the 3a dense body (3DB). 3DBs have unusual electron-dense and dynamic inner structures, and their formation is driven by the accessory protein ORF3a via hijacking a specific subset of the trans-Golgi network (TGN) and early endosomal membranes. 3DB formation is conserved in related bat and pangolin coronaviruses yet lost during the evolution to SARS-CoV. 3DBs recruit the viral structural proteins spike (S) and membrane (M) and undergo dynamic fusion/fission to facilitate efficient virion assembly. A recombinant SARS-CoV-2 virus with an ORF3a mutant specifically defective in 3DB formation showed dramatically reduced infectivity for both extracellular and cell-associated virions. Our study uncovers the crucial role of 3DB in optimal SARS-CoV-2 infectivity and highlights its potential as a target for COVID-19 prophylactics and therapeutics.

Identification of a membrane-associated element (MAE) in the C-terminal region of SARS-CoV-2 nsp6 that is essential for viral replication

The coronavirus disease 2019 (COVID-19) pandemic, caused by the novel coronavirus severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), has rapidly spread worldwide since its emergence in late 2019. Its ongoing evolution poses challenges for antiviral drug development. Coronavirus nsp6, a multiple-spanning transmembrane protein, participates in the biogenesis of the viral replication complex, which accommodates the viral replication-transcription complex. The roles of its structural domains in viral replication are not well studied. Herein, we predicted the structure of the SARS-CoV-2 nsp6 protein using AlphaFold2 and identified a highly folded C-terminal region (nsp6C) downstream of the transmembrane helices. The enhanced green fluorescent protein (EGFP)-fused nsp6C was found to cluster in the cytoplasm and associate with membranes. Functional mapping identified a minimal membrane-associated element (MAE) as the region from amino acids 237 to 276 (LGV-KLL), which is mainly composed of the α-helix H1 and the α-helix H2; the latter exhibits characteristics of an amphipathic helix (AH). Mutagenesis studies and membrane flotation experiments demonstrate that AH-like H2 is required for MAE-mediated membrane association. This MAE was functionally conserved across MERS-CoV, HCoV-OC43, HCoV-229E, HCoV-HKU1, and HCoV-NL63, all capable of mediating membrane association. In a SARS-CoV-2 replicon system, mutagenesis studies of H2 and replacements of H1 and H2 with their homologous counterparts demonstrated requirements of residues on both sides of the H2 and properly paired H1-H2 for MAE-mediated membrane association and viral replication. Notably, mutations I266A and K274A significantly attenuated viral replication without dramatically affecting membrane association, suggesting a dual role of the MAE in viral replication: mediating membrane association as well as participating in protein-protein interactions.IMPORTANCESevere acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) assembles a double-membrane vesicle (DMV) by the viral non-structural proteins for viral replication. Understanding the mechanisms of the DMV assembly is of paramount importance for antiviral development. Nsp6, a multiple-spanning transmembrane protein, plays an important role in the DMV biogenesis. Herein, we predicted the nsp6 structure of SARS-CoV-2 and other human coronaviruses using AlphaFold2 and identified a putative membrane-associated element (MAE) in the highly conserved C-terminal regions of nsp6. Experimentally, we verified a functionally conserved minimal MAE composed of two α-helices, the H1, and the amphipathic helix-like H2. Mutagenesis studies confirmed the requirement of H2 for MAE-mediated membrane association and viral replication and demonstrated a dual role of the MAE in viral replication, by mediating membrane association and participating in residue-specific interactions. This functionally conserved MAE may serve as a novel anti-viral target.

An unprecedented global challenge, emerging trends and innovations in the fight against COVID-19: A comprehensive review

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a highly contagious and dangerous virus that caused the global COVID-19 pandemic in early 2020. It primarily affects the respiratory system, leading to severe illness and high rates of mortality worldwide. The virus enters the body by binding to a receptor called ACE2, which is present in specific cells of the lungs known as type 2 alveolar epithelial cells. Numerous studies have investigated the consequences of SARS-CoV-2 infection, revealing various impacts on the body. This review provides an overview of SARS-CoV-2, including its structure and how it infects cells. It also examines the different variants of concern, such as Alpha, Beta, Gamma, Delta, and the more recent Omicron variant, discussing their characteristics and the level of damage they cause. The usage of drugs to treat COVID-19 is another aspect that has been covered and compares the effectiveness and use of antiviral drugs in the treatment and its potential benefits in COVID-19 treatment. Furthermore, this review explores the consequences and abnormalities associated with SARS-CoV-2 infection, including its impact on various organs and systems in the body. And also discussing the different COVID-19 vaccines available and their effectiveness in preventing infection and reducing the severity of illness. The current review ensures the recent update of the COVID research with expert's knowledge, collection of numerous data from reliable sources and methodologies as well as update of findings based on reviews. This review also provided clear contextual explanations to aid the interpretation and application of the results. The main motto and limitation of this manuscript are to address the computational methods of drug discovery against the rapidly evolving SARS-CoV-2 virus, which has been discussed. Additionally, current computational approaches which are cost effective and can able to predict the therapeutic agents for the treatment against the virus have also been discussed.

Who Is the Intermediate Host of RNA Viruses? A Study Focusing on SARS-CoV-2 and Poliovirus

The COVID-19 pandemic has sparked a surge in research on microbiology and virology, shedding light on overlooked aspects such as the infection of bacteria by RNA virions in the animal microbiome. Studies reveal a decrease in beneficial gut bacteria during COVID-19, indicating a significant interaction between SARS-CoV-2 and the human microbiome. However, determining the origins of the virus remains complex, with observed phenomena such as species jumps adding layers to the narrative. Prokaryotic cells play a crucial role in the disease's pathogenesis and transmission. Analyzing previous studies highlights intricate interactions from clinical manifestations to the use of the nitrogen isotope test. Drawing parallels with the history of the Poliovirus underscores the need to prioritize investigations into prokaryotic cells hosting RNA viruses.

Investigating ultrastructural morphology in MIRAGE syndrome-derived fibroblasts using transmission electron microscopy

Background

Heterozygous de novo variants in the gene SAMD9 cause the complex multisystem disorder, MIRAGE syndrome. Patients are characterised by myelodysplasia, infections, growth restriction, adrenal insufficiency, gonadal dysfunction and enteropathies. Pathogenic variants in SAMD9 are gain-of-function and enhance its role as a growth repressor, leading to growth restriction of many tissues. Two studies have reported changes in skin fibroblasts derived from MIRAGE patients, more specifically identifying enlarged endosomes. We have also previously shown subtle changes in endosome size in patients' fibroblasts compared to controls. However, these variations in endosomes were not as marked as those described in the literature.

Methods

We have performed an observational study using transmission electron microscopy (TEM) in a larger number of cells derived from three patients' fibroblasts to assess ultrastructure morphology compared to control images.

Results

Consistent changes were observed in cell organelles in all patient samples. In particular, increased endosomal activity was detected, characterised by augmented pinocytosis and vesicle budding, increased endosome number, as well as by large lysosomes and endosomes. Endoplasmic reticulum was also prominent. Mitochondria appeared enlarged in selected cells, possibly due to cellular stress. Cell nuclei did not display major differences compared to controls.

Conclusions

TEM is a powerful tool to investigate morphological features of tissues and cell organelles, although TEM data could be affected by sample preparation methodology, therefore potentially explaining the variability between independent studies, and its analysis can be dependent on the experience of the researcher. The increased endosomal activity we have observed in patients' fibroblasts could indicate that SAMD9 regulates endocytosis of receptors, acting as an endosome fusion facilitator, or in lysosomal activation. However, the precise mechanism(s) by which SAMD9 regulates cell growth is still not fully understood, and further studies are needed to elucidate its pathogenic pathway and develop therapeutic approaches to support patients.

Nucleocapsid protein accumulates in renal tubular epithelium of a post-COVID-19 patient

IMPORTANCE

Even though the coronavirus disease 2019 (COVID-19) pandemic is slowly developing into a conventional infectious disease, the long-term effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infection are still not well understood. One of the problems is that many COVID-19 cases develop acute kidney injuries. Still, it is heavily debated whether SARS-CoV-2 virus enters and actively replicates in kidney tissue and if SARS-CoV-2 virus particles can be detected in kidney during or post-infection. Here, we demonstrated that nucleocapsid N protein was detected in kidney tubular epithelium of patients that already recovered form COVID-19. The presence of the abundantly produced N protein without signs of viral replication could have implications for the recurrence of kidney disease and have a continuing effect on the immune system.

COVID-19 in Children: Molecular Profile and Pathological Features

Although the World Health Organization has declared the end of the COVID-19 pandemic, doctors continue to register new cases of the disease among both adults and children. Unfortunately, the course of COVID-19 in children can have a severe form, with death being a potential outcome. The absence of published works discussing the pathological morphology of COVID-19 in children prevents the objective analysis of the disease's pathogenesis, including among the adult population. In this vein, the objective of our study is to identify the morphological features of the lungs' involvement and evaluate virus-host interactions in the case of COVID-19 in patients at a pediatric medical practice. We present the results of the study of the lungs of three children who died due to COVID-19, highlighting the predominant involvement of their respiratory organs at different stages of the disease (5, 21, and 50 days). This article presents data obtained from histopathological and immunohistochemical investigations, taking into account the results of clinical and laboratory indicators and intravital and postmortem SARS-CoV-2 PCR investigations. The common finding of all of the examined COVID-19 cases is the involvement of the endothelium in microcirculation vessels, which are considered to be a primary target of various pathogenic influencing factors. We also discuss both the significance of apoptosis as a result of virus-host interactions and the most likely cause of endothelium cell destruction. The results of this study could be useful for the development of endothelium-protective therapy to prevent the progression of disseminated intravascular coagulation syndrome.

Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions

The latest RNA genomic mutation of SARS-CoV-2 virus, termed the Omicron variant, has generated a stream of highly contagious and antibody-resistant strains, which in turn led to classifying Omicron as a variant of concern. We systematically collected Raman spectra from six Omicron subvariants available in Japan (i.e., BA.1.18, BA.2, BA.4, BA.5, XE, and BA.2.75) and applied machine-learning algorithms to decrypt their structural characteristics at the molecular scale. Unique Raman fingerprints of sulfur-containing amino acid rotamers, RNA purines and pyrimidines, tyrosine phenol ring configurations, and secondary protein structures clearly differentiated the six Omicron subvariants. These spectral characteristics, which were linked to infectiousness, transmissibility, and propensity for immune evasion, revealed evolutionary motifs to be compared with the outputs of genomic studies. The availability of a Raman "metabolomic snapshot", which was then translated into a barcode to enable a prompt subvariant identification, opened the way to rationalize in real-time SARS-CoV-2 activity and variability. As a proof of concept, we applied the Raman barcode procedure to a nasal swab sample retrieved from a SARS-CoV-2 patient and identified its Omicron subvariant by coupling a commercially available magnetic bead technology with our newly developed Raman analyses.

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

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

Coronaviruses spike glycoprotein endodomains: The sequence and structure-based comprehensive study

Any protein's flexibility or region makes it available to interact with many biomolecules in the cell. Specifically, such interactions in viruses help them to perform more functions despite having a smaller genome. Therefore, these flexible regions can be exciting and essential targets to be explored for their role in pathogenicity and therapeutic developments as they achieve essential interactions. In the continuation with our previous study on disordered analysis of SARS-CoV-2 spike protein's cytoplasmic tail (CTR), or endodomain, here we have explored the endodomain's disordered potential of six other coronaviruses using multiple bioinformatics approaches and molecular dynamics simulations. Based on the comprehensive analysis of its sequence and structural composition, we report the varying disorder propensity in endodomains of spike proteins of coronaviruses. The observations of this study may help to understand the importance of spike glycoprotein endodomain and creating therapeutic interventions against them.

Re-Emerging COVID-19: Controversy of Its Zoonotic Origin, Risks of Severity of Reinfection and Management

The re-emergence of COVID-19 has sparked controversy around its zoonotic origin, management strategies, risks posed by the virus, and the severity of reinfection. While it is widely accepted that the virus originated from animals, the exact source and transmission pathway remain unclear. This has led to debates regarding the regulation of wildlife markets and trade, as well as the need for more robust surveillance and monitoring systems. Hence, the objective of this review is to provide a brief overview of the disease's biology, preventative strategies, risk factors, degree of reinfection, and epidemiological profile. It offers a thorough examination of the disease's root cause, potential zoonotic transmission, and the most recent preventive measures, like vaccines. In terms of management, there is ongoing debate about the most effective strategies to mitigate the spread of the virus. While public health measures such as social distancing and mask-wearing have been widely implemented, there are differing opinions on the effectiveness of lockdowns and restrictions on public movement. The risks posed by COVID-19 are also a topic of debate, with some arguing that the virus is relatively low-risk for the majority of the population while others highlight the potential for severe illness, particularly among vulnerable populations such as the elderly or those with underlying health conditions. Finally, the possibility of reinfection has raised concerns about the longevity of immunity following infection or vaccination. While some studies have suggested that reinfection may be possible and potentially more severe, the overall risk remains uncertain and further research is needed to fully understand the implications of reinfection.

Molecular insight of phytocompounds from Indian spices and its hyaluronic acid conjugates to block SARS-CoV-2 viral entry

Human corona viral infection leads to acute breathing disease and death if not diagnosed and treated properly in time. The disease can be treated with the help of simple natural compounds, which we use in day-to-day life. These natural compounds act against several diseases but their drug targeting mechanism needs to be improved for more efficient and promising applications. In the present study five compounds (gingerol, thymol, thymohydroquinone, cyclocurcumin, hydrazinocurcumin) from three Indian medicinal plants (ginger, black cumin, turmeric) and its hyaluronic acid (HA) conjugates were docked against initially deposited spike structural proteins (PDB ID 6WPT) and its mutant variant D-614G (PDB ID 6XS6). Docking study result reveals that all the HA conjugates showed the most effective inhibitor of S-protein of initially deposited and D-614G variant forms of SARS-CoV-2. The compounds like Gingerol, Thymol, Thymohydroquinone, Cyclocurcumin, Hydrazinocurcumin, Hydroxychloroquinone, and hyaluronic acid conjugates inhibit the viral protein of both wild-type and mutated S-protein of SARS-CoV-2. The molecular docking studies of phytocompounds with initial deposited and variant spike protein targets show superior binding affinity than with the commercial repurposed viral entry inhibitor hydroxychloroquine. Further, the docking result was modeled using MD simulation study shows excellent simulation trajectories between spike proteins and HA conjugates spices constituents than its free form. DFT analysis was carried out to affirm the reason behind the highest binding affinity of HA conjugates over its free form towards SARS-CoV-2 spike protein targets. Further HA conjugates synthesis and its evaluation against SARS-CoV-2 in vitro studies are needed to prove our novel idea for an anti-viral drug.Communicated by Ramaswamy H. Sarma.

Severe Acute Respiratory Syndrome Coronavirus 2 Vasculopathy in a Syrian Golden Hamster Model

Clinical evidence of vascular dysfunction and hypercoagulability as well as pulmonary vascular damage and microthrombosis are frequently reported in severe cases of human coronavirus disease 2019 (COVID-19). Syrian golden hamsters recapitulate histopathologic pulmonary vascular lesions reported in patients with COVID-19. Herein, special staining techniques and transmission electron microscopy further define vascular pathologies in a Syrian golden hamster model of human COVID-19. The results show that regions of active pulmonary inflammation in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are characterized by ultrastructural evidence of endothelial damage with platelet marginalization and both perivascular and subendothelial macrophage infiltration. SARS-CoV-2 antigen/RNA was not detectable within affected blood vessels. Taken together, these findings suggest that the prominent microscopic vascular lesions in SARS-CoV-2-inoculated hamsters likely occur due to endothelial damage followed by platelet and macrophage infiltration.

Statins: Beneficial Effects in Treatment of COVID-19

The recent viral disease COVID-19 has attracted much attention. The disease is caused by SARS-CoV-19 virus which has different variants and mutations. The mortality rate of SARS-CoV-19 is high and efforts to establish proper therapeutic solutions are still ongoing. Inflammation plays a substantial part in the pathogenesis of this disease causing mainly lung tissue destruction and eventually death. Therefore, anti-inflammatory drugs or treatments that can inhibit inflammation are important options. Various inflammatory pathways such as nuclear factor Kappa B (NF-κB), signal transducer of activators of transcription (STAT), nod-like receptor family protein 3 (NLRP), toll-like receptors (TLRs), mitogen-activated protein kinase (MAPK), and mammalian target of rapamycin (mTOR) pathways and mediators, such as interleukin (IL)-6, IL-1β, tumor necrosis factor-α (TNF-α), and interferon-γ (INF-γ), cause cell apoptosis, reduce respiratory capacity and oxygen supply, eventually inducing respiratory system failure and death. Statins are well known for controlling hypercholesterolemia and may serve to treat COVID-19 due to their pleiotropic effects among which are anti-inflammatory in nature. In this chapter, the anti-inflammatory effects of statins and their possible beneficial effects in COVID-19 treatment are discussed. Data were collected from experimental and clinical studies in English (1998-October 2022) from Google Scholar, PubMed, Scopus, and the Cochrane Library.

Near-Native Visualization of SARS-CoV-2 Induced Membrane Remodeling and Virion Morphogenesis

Infection with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of the COVID-19 pandemic, leads to profound remodeling of cellular membranes, promoting viral replication and virion assembly. A full understanding of this drastic remodeling and the process of virion morphogenesis remains lacking. In this study, we applied room temperature transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) tomography to visualize the SARS-CoV-2 replication factory in Vero cells, and present our results in comparison with published cryo-EM studies. We obtained cryo-EM-like clarity of the ultrastructure by employing high-pressure freezing, freeze substitution (HPF-FS) and embedding, allowing room temperature visualization of double-membrane vesicles (DMVs) in a near-native state. In addition, our data illustrate the consecutive stages of virion morphogenesis and reveal that SARS-CoV-2 ribonucleoprotein assembly and membrane curvature occur simultaneously. Finally, we show the tethering of virions to the plasma membrane in 3D, and that accumulations of virus particles lacking spike protein in large vesicles are most likely not a result of defective virion assembly at their membrane. In conclusion, this study puts forward a room-temperature EM technique providing near-native ultrastructural information about SARS-CoV-2 replication, adding to our understanding of the interaction of this pandemic virus with its host cell.

Chest CT in covid-19 pneumonia's follow-up: A 30 patients case series

Background

Lung abnormalities do not fully resolve in all Covid-19 survivors and may progress to fibrosis. Understanding post-COVID lung changes helps identify patients susceptible of post-COVID-19 sequelae. We analyzed scannographic residual lung abnormalities and the full resolution percentage on intermediate- and long-term follow-up (3 months or more).

Methods

Data from 30 RT-PCR positive COVID-19 patients undergoing at least one follow-up chest CT at Ibn Sina Hospital, with a minimal time interval of 3 months between the RT-PCR and the CT performance were gathered retrospectively. The following elements were analyzed: (1) lung opacities, (2) distribution, (3) dominant lung opacity, (4) Sub-pleural bands, (5) Interlobular septal thickening, (6) Vascular dilatation, (7) Bronchiectasis, (8) Honey combing, (9) Architectural distortion, (10) mosaic attenuation, and (11) Additional findings: Enlarged lymph nodes, Pleural and Pericardial fluid. To evaluate the degree of lung opacification, a score founded on visual evaluation of the lung involvement's percentage was employed. Patients were then subdivided into two categories: (1) no residual opacities and (2) remaining pulmonary opacities.

Outcomes

30 patients were enrolled. The age ranged between 40 and 87 years. CT was indicated for symptoms or functional impairment. The time range between the positive RT-PCR and Follow-up CT varied between 3 and 12 months. CT severity score ranged between o and 23. Residual lung opacities were present in 24 cases (80%). The dominant lung opacities were Ground glass (46.7%), and linear/curvilinear opacities (23.3%). Signs of fibrosis were present in 9 patients (30%).

Conclusion

CT abnormalities following Covid-19 pneumonia's prevalence varies based on the extent of the original lung affection and the time gap since the acute phase. Residual anomalies' effects on respiratory physiology, symptoms, and quality of living are unknown. Maintained monitoring of COVID-19 survivors with clinical examination, iterative pulmonary function tests, and HRCT is advised.

Ultraviolet dosage and decontamination efficacy were widely variable across 14 UV devices after testing a dried enveloped ribonucleic acid virus surrogate for SARS-CoV-2

Aims: The dosages and efficacy of 14 ultraviolet (UV) decontamination technologies were measured against a SARS-CoV-2 surrogate virus that was dried onto different materials for laboratory and field testing. Methods and results: A live enveloped, ribonucleic acid (RNA) virus surrogate for SARS-CoV-2 was dried on stainless steel 304 (SS304), Navy Top Coat-painted SS304 (NTC), cardboard, polyurethane, polymethyl methacrylate (PMMA), and acrylonitrile butadiene styrene (ABS) materials at > 8.0 log10 plaque-forming units (PFU) per test coupon. The coupons were then exposed to UV radiation during both laboratory and field testing. Commercial and prototype UV-emitting devices were measured for efficacy: four handheld devices, three room/surface-disinfecting machines, five air disinfection devices, and two larger custom-made machines. UV device dosages ranged from 0.01 to 729 mJ cm-2. The antiviral efficacy among the different UV devices ranged from no decontamination up to nearly achieving sterilization. Importantly, cardboard required far greater dosage than SS304. Conclusion: Enormous variability in dosage and efficacy was measured among the different UV devices. Porous materials limit the utility of UV decontamination. Significance and impact of the study: UV devices have wide variability in dosages, efficacy, hazards, and UV output over time, indicating that each UV device needs independent technical measurement and assessment for product development prior to and during use.

Ultrastructural analysis and three-dimensional reconstruction of cellular structures involved in SARS-CoV-2 spread

The cytoskeleton not only deals with numerous interaction and communication mechanisms at the cellular level but also has a crucial role in the viral infection cycle. Although numerous aspects of SARS-CoV-2 virus interaction at the cellular level have been widely studied, little has been reported about the structural and functional response of the cytoskeleton. This work aims to characterize, at the ultrastructural level, the modifications in the cytoskeleton of infected cells, namely, its participation in filopodia formation, the junction of these nanostructures forming bridges, the viral surfing, and the generation of tunnel effect nanotubes (TNT) as probable structures of intracellular viral dissemination. The three-dimensional reconstruction from the obtained micrographs allowed observing viral propagation events between cells in detail for the first time. More profound knowledge about these cell-cell interaction models in the viral spread mechanisms could lead to a better understanding of the clinical manifestations of COVID-19 disease and to find new therapeutic strategies.

Thiopurines inhibit coronavirus Spike protein processing and incorporation into progeny virions

There is an outstanding need for broadly acting antiviral drugs to combat emerging viral diseases. Here, we report that thiopurines inhibit the replication of the betacoronaviruses HCoV-OC43 and SARS-CoV-2. 6-Thioguanine (6-TG) disrupted early stages of infection, limiting accumulation of full-length viral genomes, subgenomic RNAs and structural proteins. In ectopic expression models, we observed that 6-TG increased the electrophoretic mobility of Spike from diverse betacoronaviruses, matching the effects of enzymatic removal of N-linked oligosaccharides from Spike in vitro. SARS-CoV-2 virus-like particles (VLPs) harvested from 6-TG-treated cells were deficient in Spike. 6-TG treatment had a similar effect on production of lentiviruses pseudotyped with SARS-CoV-2 Spike, yielding pseudoviruses deficient in Spike and unable to infect ACE2-expressing cells. Together, these findings from complementary ectopic expression and infection models strongly indicate that defective Spike trafficking and processing is an outcome of 6-TG treatment. Using biochemical and genetic approaches we demonstrated that 6-TG is a pro-drug that must be converted to the nucleotide form by hypoxanthine phosphoribosyltransferase 1 (HPRT1) to achieve antiviral activity. This nucleotide form has been shown to inhibit small GTPases Rac1, RhoA, and CDC42; however, we observed that selective chemical inhibitors of these GTPases had no effect on Spike processing or accumulation. By contrast, the broad GTPase agonist ML099 countered the effects of 6-TG, suggesting that the antiviral activity of 6-TG requires the targeting of an unknown GTPase. Overall, these findings suggest that small GTPases are promising targets for host-targeted antivirals.

The COVID-19 pandemic has ignited efforts to repurpose existing drugs as safe and effective antivirals. Rather than directly inhibiting viral enzymes, host-targeted antivirals inhibit host cell processes to indirectly impede viral replication and/or stimulate antiviral responses. Here, we describe a new antiviral mechanism of action for an FDA-approved thiopurine known as 6-thioguanine (6-TG). We demonstrate that 6-TG is a pro-drug that must be metabolized by host enzymes to gain antiviral activity. We show that it can inhibit the replication of human coronaviruses, including SARS-CoV-2, at least in part by interfering with the processing and accumulation of Spike glycoproteins, thereby impeding assembly of infectious progeny viruses. We provide evidence implicating host cell GTPase enzymes in the antiviral mechanism of action.

A systemic review on liquid crystals, nanoformulations and its application for detection and treatment of SARS - CoV- 2 (COVID - 19)

The COVID-19 is a pandemic caused by the SARS-CoV-2 virus, has instigated major health problems and prompted WHO to proclaim a worldwide medical emergency. The knowledge of SARS-CoV-2 fundamental structure, aetiology, its entrance mechanism, membrane hijacking and immune response against the virus, are important parameters to develop effective vaccines and medicines. Liquid crystals integrated nano-techniques and various nanoformulations were applied to tackle the severity of the virus. It was reported that nanoformulations have helped to enhance the effectiveness of presently accessible antiviral medicines or to elicit a fast immunological response against COVID-19 virus. Applications of liquid crystals, nanostructures, nanoformulations and nanotechnology in diagnosis, prevention, treatment and tailored vaccine administration against COVID-19 which will help in establishing the framework for a successful pandemic combat are reviewed. This review also focuses on limitations associated with liquid crystal-nanotechnology based systems and suggests the possible ways to address these limitations. Also, topical advancements in the ground of liquid crystals and nanostructures established diagnostics (nanosensor/biosensor) are discussed in detail.

Ultrastructural Characterization of Human Bronchial Epithelial Cells during SARS-CoV-2 Infection: Morphological Comparison of Wild-Type and CFTR-Modified Cells

SARS-CoV-2 replicates in host cell cytoplasm. People with cystic fibrosis, considered at risk of developing severe symptoms of COVID-19, instead, tend to show mild symptoms. We, thus, analyzed at the ultrastructural level the morphological effects of SARS-CoV-2 infection on wild-type (WT) and F508del (ΔF) CFTR-expressing CFBE41o- cells at early and late time points post infection. We also investigated ACE2 expression through immune-electron microscopy. At early times of infection, WT cells exhibited double-membrane vesicles, representing typical replicative structures, with granular and vesicular content, while at late time points, they contained vesicles with viral particles. ∆F cells exhibited double-membrane vesicles with an irregular shape and degenerative changes and at late time of infection, showed vesicles containing viruses lacking a regular structure and a well-organized distribution. ACE2 was expressed at the plasma membrane and present in the cytoplasm only at early times in WT, while it persisted even at late times of infection in ΔF cells. The autophagosome content also differed between the cells: in WT cells, it comprised vesicles associated with virus-containing structures, while in ΔF cells, it comprised ingested material for lysosomal digestion. Our data suggest that CFTR-modified cells infected with SARS-CoV-2 have impaired organization of normo-conformed replicative structures.

Assessing and improving the validity of COVID-19 autopsy studies - A multicentre approach to establish essential standards for immunohistochemical and ultrastructural analyses

Background

Autopsy studies have provided valuable insights into the pathophysiology of COVID-19. Controversies remain about whether the clinical presentation is due to direct organ damage by SARS-CoV-2 or secondary effects, such as overshooting immune response. SARS-CoV-2 detection in tissues by RT-qPCR and immunohistochemistry (IHC) or electron microscopy (EM) can help answer these questions, but a comprehensive evaluation of these applications is missing.

Methods

We assessed publications using IHC and EM for SARS-CoV-2 detection in autopsy tissues. We systematically evaluated commercially available antibodies against the SARS-CoV-2 proteins in cultured cell lines and COVID-19 autopsy tissues. In a multicentre study, we evaluated specificity, reproducibility, and inter-observer variability of SARS-CoV-2 IHC. We correlated RT-qPCR viral tissue loads with semiquantitative IHC scoring. We used qualitative and quantitative EM analyses to refine criteria for ultrastructural identification of SARS-CoV-2.

Findings

Publications show high variability in detection and interpretation of SARS-CoV-2 abundance in autopsy tissues by IHC or EM. We show that IHC using antibodies against SARS-CoV-2 nucleocapsid yields the highest sensitivity and specificity. We found a positive correlation between presence of viral proteins by IHC and RT-qPCR-determined SARS-CoV-2 viral RNA load (N= 35; r=-0.83, p-value <0.0001). For EM, we refined criteria for virus identification and provide recommendations for optimized sampling and analysis. 135 of 144 publications misinterpret cellular structures as virus using EM or show only insufficient data. We provide publicly accessible digitized EM sections as a reference and for training purposes.

Interpretation

Since detection of SARS-CoV-2 in human autopsy tissues by IHC and EM is difficult and frequently incorrect, we propose criteria for a re-evaluation of available data and guidance for further investigations of direct organ effects by SARS-CoV-2.

Funding

German Federal Ministry of Health, German Federal Ministry of Education and Research, Berlin University Alliance, German Research Foundation, German Center for Infectious Research.

Rapid and sensitive detection of viral particles by coupling redox cycling and electrophoretic enrichment

The COVID-19 pandemic has highlighted the need for rapid, low-cost, and sensitive virus detection platforms to monitor and mitigate widespread outbreaks. Electrochemical sensors are a viable choice to fill this role but still require improvements to the signal magnitude, especially for early detection and low viral loads. Herein, finite element analysis of a novel biosensor concept for single virion counting using a generator-collector microelectrode design is presented. The proposed design combines a redox-cycling amplified electrochemical current with electrophoresis-driven electrode-particle collision for rapid virus detection. The effects of experimental (e.g. scan rate, collector bias) and geometric factors are studied to optimize the sensor design. Two generator-collector configurations are explored: a ring-disk configuration to analyze sessile droplets and an interdigitated electrode (IDE) design housed in a microchannel. For the ring-disk configuration, we calculate an amplification factor of ∼5 and collector efficiency of ∼0.8 for a generator-collector spacing of 600 nm. For the IDE, the collector efficiency is even larger, approaching unity. The dual-electrode mode is critical for increasing the current and electric field strength. As a result, the current steps upon virus capture are more than an order of magnitude larger compared to single-mode. Additionally, single virus capture times are reduced from over 700 s down to ∼20 s. Overall, the frequency of virus capture and magnitude of the electrochemical current steps depend on the virus properties and electrode configuration, with the IDE capable of single virus detection within seconds owing to better particle confinement in the microchannel.

A global lipid map reveals host dependency factors conserved across SARS-CoV-2 variants

A comprehensive understanding of host dependency factors for SARS-CoV-2 remains elusive. Here, we map alterations in host lipids following SARS-CoV-2 infection using nontargeted lipidomics. We find that SARS-CoV-2 rewires host lipid metabolism, significantly altering hundreds of lipid species to effectively establish infection. We correlate these changes with viral protein activity by transfecting human cells with each viral protein and performing lipidomics. We find that lipid droplet plasticity is a key feature of infection and that viral propagation can be blocked by small-molecule glycerolipid biosynthesis inhibitors. We find that this inhibition was effective against the main variants of concern (alpha, beta, gamma, and delta), indicating that glycerolipid biosynthesis is a conserved host dependency factor that supports this evolving virus.

Identification of coronavirus particles by electron microscopy: a complementary tool for deciphering COVID-19

We thank C. Dittmayer and M. Laue for giving us the opportunity to clarify issues regarding the identification of coronavirus (CV) particles by electron microscopy (EM) demonstrated in our recent publication [1]. We would like to respond to the authors’ statements, as follows:

Identification of coronavirus particles by electron microscopy: a complementary tool for deciphering COVID-19 https://bit.ly/3Kk5PT8

Antiviral Biodegradable Food Packaging and Edible Coating Materials in the COVID-19 Era: A Mini-Review

With the onset of the COVID-19 pandemic in late 2019, and the catastrophe faced by the world in 2020, the food industry was one of the most affected industries. On the one hand, the pandemic-induced fear and lockdown in several countries increased the online delivery of food products, resulting in a drastic increase in single-use plastic packaging waste. On the other hand, several reports revealed the spread of the viral infection through food products and packaging. This significantly affected consumer behavior, which directly influenced the market dynamics of the food industry. Still, a complete recovery from this situation seems a while away, and there is a need to focus on a potential solution that can address both of these issues. Several biomaterials that possess antiviral activities, in addition to being natural and biodegradable, are being studied for food packaging applications. However, the research community has been ignorant of this aspect, as the focus has mainly been on antibacterial and antifungal activities for the enhancement of food shelf life. This review aims to cover the different perspectives of antiviral food packaging materials using established technology. It focuses on the basic principles of antiviral activity and its mechanisms. Furthermore, the antiviral activities of several nanomaterials, biopolymers, natural oils and extracts, polyphenolic compounds, etc., are discussed.

Coronavirus-A Crippling Affliction to Humans

Coronaviruses hold idiosyncratic morphological features and functionality. The members of this group have a remarkable capability of infecting both animals and humans. Inimitably, the replication of the RNA genome continues through the set of viral mRNA molecules. Coronaviruses received the least attention until 2003 since they caused only minor respiratory tract illnesses. However, this changed exclusively with the introduction of zoonotic SARS-CoV in 2003. In 2012, MERS-CoV emerged and confirmed this group of viruses as the major causative agents of severe respiratory tract illness. Today, Coronavirus Disease 2019 (i.e., COVID-19) has turned out to be a chief health problem that causes a severe acute respiratory disorder in humans. Since the first identification of COVID-19 in December 2019 in Wuhan, China, this infection has devastatingly spread all around the globe leading to a crippling affliction for humans. The strain is known as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), and WHO (the World Health Organization) has termed this new pandemic disease as Coronavirus Disease (COVID-19). COVID-19 is still spreading, with an estimated 136 million confirmed cases and more than 2.94 million deaths worldwide so far while the pandemic is still going on. In the current scenario, there is no particular treatment for COVID-19, however remarkable efforts for immunization and vaccine development can be observed. Therefore, the execution of precautions and proper preventive measures are indispensable to minimize and control the community transmission of the virus. This review summarizes information about the pathophysiology, transmission, symptoms, and the host defense mechanism as well as immunization and vaccine development against COVID-19.

Detection and identification of coronaviruses in human tissues using electron microscopy

The identification of viral particles within a tissue specimen requires specific knowledge of viral ultrastructure and replication, as well as a thorough familiarity with normal subcellular organelles. The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic has underscored how challenging the task of identifying coronavirus by electron microscopy (EM) can be. Numerous articles have been published mischaracterizing common subcellular structures, including clathrin‐ or coatomer‐ coated vesicles, multivesicular bodies, and rough endoplasmic reticulum, as coronavirus particles in SARS‐CoV‐2 positive patient tissue specimens. To counter these misinterpretations, we describe the morphological features of coronaviruses that should be used to differentiate coronavirus particles from subcellular structures. Further, as many of the misidentifications of coronavirus particles have stemmed from attempts to attribute tissue damage to direct infection by SARS‐CoV‐2, we review articles describing ultrastructural changes observed in specimens from SARS‐CoV‐2‐infected individuals that do not necessarily provide EM evidence of direct viral infection. Ultrastructural changes have been observed in respiratory, cardiac, kidney, and intestinal tissues, highlighting the widespread effects that SARS‐CoV‐2 infection may have on the body, whether through direct viral infection or mediated by SARS‐CoV‐2 infection‐induced inflammatory and immune processes.

Viroporins: Structure, function, and their role in the life cycle of SARS-CoV-2

Viroporins are indispensable for viral replication. As intracellular ion channels they disturb pH gradients of organelles and allow Ca²⁺ flux across ER membranes. Viroporins interact with numerous intracellular proteins and pathways and can trigger inflammatory responses. Thus, they are relevant targets in the search for antiviral drugs. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) underlies the world-wide pandemic of COVID-19, where an effective therapy is still lacking despite impressive progress in the development of vaccines and vaccination campaigns. Among the 29 proteins of SARS-CoV-2, the E- and ORF3a proteins have been identified as viroporins that contribute to the massive release of inflammatory cytokines observed in COVID-19. Here, we describe structure and function of viroporins and their role in inflammasome activation and cellular processes during the virus replication cycle. Techniques to study viroporin function are presented, with a focus on cellular and electrophysiological assays. Contributions of SARS-CoV-2 viroporins to the viral life cycle are discussed with respect to their structure, channel function, binding partners, and their role in viral infection and virus replication. Viroporin sequences of new variants of concern (α–ο) of SARS-CoV-2 are briefly reviewed as they harbour changes in E and 3a proteins that may affect their function.

Effectiveness of N95 Masks against SARS-CoV-2: Performance Efficiency, Concerns, and Future Directions

The coronavirus disease 2019 (COVID-19) epidemic, which is caused by novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has continued to spread around the world since December 2019. Healthcare workers and other medical first responders in particular need personal protective equipment to protect their respiratory system from airborne particulates, in addition to liquid splashes to the face. N95 respirator have become a critical component for reducing SARS-CoV-2 transmission and controlling the scale of the COVID-19 pandemic. However, a major dispute concerning the protective performance of N95 respirators has erupted, with a myriad of healthcare workers affected despite wearing N95 masks. This article reviews the most recent updates about the performance of N95 respirators in protecting against the SARS-CoV-2 virus in the present pandemic situation. A brief overview of the manufacturing methods, air filtration mechanisms, stability, and reusability of the mask is provided. A detailed performance evaluation of the mask is studied from an engineering point of view. This Review also reports on a comparative study about the protective performance of all commercially available surgical and respiratory masks used to combat the spread of COVID-19. With the aim of protecting healthcare providers more efficiently, we suggest some potential directions for the development of this respiratory mask that improve the performance efficiency of the mask.

Spectroscopy: a versatile sensing tool for cost-effective and rapid detection of novel coronavirus (COVID-19)

The deadly novel coronavirus SARS-CoV-2 is responsible for COVID-19, which was first recognized in Wuhan, China, in December 2019. Rapid identification at primary stage of the novel coronavirus, SARS-CoV-2, is important to restrict it and prevent the pandemic. Real-time RT-PCR assays are the best diagnostic tests presently available for SARS-CoV-2 detection, which are highly sensitive, even though expensive equipment and trained technicians are necessary. Furthermore, the method has moderately long time bound. This deadly viral infection can also be detected by applying various spectroscopic techniques as spectroscopy can provide fast, precise identification and monitoring, leading to the overall understanding of its mutation rates, which will further facilitate antiviral drug development as well as vaccine development. It is an innovative and non-invasive technique for combating the spread of novel coronavirus. This review article demonstrates the application of various spectroscopic techniques to detect COVID-19 rapidly. Different spectroscopy-based detection protocols and additional development of new, novel sensors and biosensors along with diagnostic kits had been described here stressing the status of sensitive diagnostic systems to handle with the COVID-19 outbreak.

Graphical abstract

Spectroscopy: A versatile sensing tool for cost-effective and rapid detection of novel Coronavirus (COVID-19).

Multi-color super-resolution imaging to study human coronavirus RNA during cellular infection

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third human coronavirus within 20 years that gave rise to a life-threatening disease and the first to reach pandemic spread. To make therapeutic headway against current and future coronaviruses, the biology of coronavirus RNA during infection must be precisely understood. Here, we present a robust and generalizable framework combining high-throughput confocal and super-resolution microscopy imaging to study coronavirus infection at the nanoscale. Using the model human coronavirus HCoV-229E, we specifically labeled coronavirus genomic RNA (gRNA) and double-stranded RNA (dsRNA) via multi-color RNA immunoFISH and visualized their localization patterns within the cell. The 10-nm resolution achieved by our approach uncovers a striking spatial organization of gRNA and dsRNA into three distinct structures and enables quantitative characterization of the status of the infection after antiviral drug treatment. Our approach provides a comprehensive imaging framework that will enable future investigations of coronavirus fundamental biology and therapeutic effects.

A global lipid map reveals host dependency factors conserved across SARS-CoV-2 variants

A comprehensive understanding of host dependency factors for SARS-CoV-2 remains elusive. We mapped alterations in host lipids following SARS-CoV-2 infection using nontargeted lipidomics. We found that SARS-CoV-2 rewires host lipid metabolism, altering 409 lipid species up to 64-fold relative to controls. We correlated these changes with viral protein activity by transfecting human cells with each viral protein and performing lipidomics. We found that lipid droplet plasticity is a key feature of infection and that viral propagation can be blocked by small-molecule glycerolipid biosynthesis inhibitors. We found that this inhibition was effective against the main variants of concern (alpha, beta, gamma, and delta), indicating that glycerolipid biosynthesis is a conserved host dependency factor that supports this evolving virus.

Characterization of the First SARS-CoV-2 Isolates from Aotearoa New Zealand as Part of a Rapid Response to the COVID-19 Pandemic

SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has wreaked havoc across the globe for the last two years. More than 300 million cases and over 5 million deaths later, we continue battling the first real pandemic of the 21st century. SARS-CoV-2 spread quickly, reaching most countries within the first half of 2020, and New Zealand was not an exception. Here, we describe the first isolation and characterization of SARS-CoV-2 variants during the initial virus outbreak in New Zealand. Patient-derived nasopharyngeal samples were used to inoculate Vero cells and, three to four days later, a cytopathic effect was observed in seven viral cultures. Viral growth kinetics was characterized using Vero and VeroE6/TMPRSS2 cells. The identity of the viruses was verified by RT-qPCR, Western blot, indirect immunofluorescence assays, and electron microscopy. Whole-genome sequences were analyzed using two different yet complementary deep sequencing platforms (MiSeq/Illumina and Ion PGM™/Ion Torrent™), classifying the viruses as SARS-CoV-2 B.55, B.31, B.1, or B.1.369 based on the Pango Lineage nomenclature. All seven SARS-CoV-2 isolates were susceptible to remdesivir (EC₅₀ values from 0.83 to 2.42 µM) and β-D-N⁴-hydroxycytidine (molnupiravir, EC₅₀ values from 0.96 to 1.15 µM) but not to favipiravir (>10 µM). Interestingly, four SARS-CoV-2 isolates, carrying the D614G substitution originally associated with increased transmissibility, were more susceptible (2.4-fold) to a commercial monoclonal antibody targeting the spike glycoprotein than the wild-type viruses. Altogether, this seminal work allowed for early access to SARS-CoV-2 isolates in New Zealand, paving the way for numerous clinical and scientific research projects in the country, including the development and validation of diagnostic assays, antiviral strategies, and a national COVID-19 vaccine development program.

Hand sanitizers as a preventive measure in COVID-19 pandemic, its characteristics, and harmful effects: a review

Background

In the global health emergency caused by COVID-19, multiple experts have mandated the use of hand sanitizers as a safety measure from COVID-19. The sale of hand sanitizers has increased many folds. Therefore, when there is such large use of hand sanitizers, it becomes extremely important to study and understand hand sanitizers in a comprehensive manner.

Main body of the abstract

This article starts with the importance of sanitizers as a defence mechanism that is employed by the hand to fight against the coronavirus. This article provides information about history, types, composition, various dosage forms, and marketed formulations of hand sanitizers. The article sheds a detailed light on industrial production techniques for hand sanitizers and also outlines new innovative techniques that were employed by the industry to mass produce hand sanitizers in the wake of the pandemic. The article further dives into a comparison between hand sanitizers and soaps so as to give pros and cons of the use of soap against the use of hand sanitizers. One of the aims of the article is to study the side effects of sanitizers so as to develop a cautious approach while using hand sanitizers and therefore a comprehensive list of side effects of the use of hand sanitizers is given.

Conclusion

The review article finds that hand sanitizers are extremely efficient in fight the virus but along with it, it brings along arrange of risks which are outlined in the article.

COVID-19: inflammatory responses, structure-based drug design and potential therapeutics

The COVID-19 pandemic caused by SARS-CoV-2 is responsible for the global health emergency. Here, we explore the diverse mechanisms of SARS-CoV-induced inflammation. We presume that SARS-CoV-2 likely contributes analogous inflammatory responses. Possible therapeutic mechanisms for reducing SARS-CoV-2-mediated inflammatory responses comprise FcR inactivation. Currently, there is no specific remedy available against the SARS-CoV-2. Consequently, recognizing efficacious antiviral leads to combat the virus is crucially desired. The coronavirus (CoV) main protease (Mpro also called 3CLpro), which plays an indispensable role in viral replication and transcription, is an interesting target for drug design. This review compiles the latest advances in biological and structural research, along with development of inhibitors targeting CoV Mpros. It is anticipated that inhibitors targeting CoV Mpros could be advanced into wide-spectrum antiviral drugs in case of COVID-19 and other CoV-related diseases. The crystal structural and docking results have shown that Ebselen, N3, TDZD-8 and α-ketoamide (13b) inhibitors can bind to the substrate-binding pocket of COVID-19 Mpro. α-ketoamide-based inhibitor 13b inhibits the replication of SARS-CoV-2 in human Calu3 lung cells. Quantitative real-time RT-PCR (qRT-PCR) showed that the treatment with Ebselen, TDZD-8 and N3 reduced the amounts of SARS-CoV-2, respectively, 20.3-, 10.19- and 8.4-fold compared to the treatment in the absence of inhibitor. Moreover, repurposing of already present drugs to treat COVID-19 serves as one of the competent and economic therapeutic strategies. Several anti-malarial, anti-HIV and anti-inflammatory drugs as mentioned in Table 2 were found effective for the COVID-19 treatment. Further, hydroxychloroquine (HCQ) was found more potent than chloroquine (CQ) in inhibiting SARS-CoV-2 in vitro. Furthermore, convalescent plasma from patients who have recuperated from viral infections can be employed as a therapy without the appearance of severe adverse events. Hence, it might be valuable to examine the safety and efficacy of convalescent plasma transfusion in SARS-CoV-2-infected patients.

A Standardization Protocol for the In Situ Detection of SARS-CoV2 RNA and Proteins

This manuscript details a stringent protocol for the in situ detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) RNA and 4 different viral proteins: envelope, spike, membrane, and nucleocapsid. Key aspects of the protocol are: (1) analysis of adjacent (serial) sections for viral RNA and at least 2 viral proteins; (2) cytologic alterations in the cells scored as virus positive based on an hematoxylin and eosin stain; (3) in situ demonstration of a host response in the cells scored as virus positive; (4) co-labeling experiments that show that the viral RNA and/or proteins co-localize with each other and the angiotensin converting enzyme 2 (ACE2) receptor; and (5) lack of signal in equivalent tissues obtained before the pandemic. Optimization conditions for the four viral proteins as well as the ACE2 receptor were each antigen retrieval in an EDTA solution which facilitates co-expression analyses. It is recommended not to use either electron microscopy or qRTPCR as methods to corroborate in situ SARS-CoV2 detection. This stringent protocol, that relies on sequentially labeled serial sections and can be completed in one working day, demonstrated the following: (1) infectious SARS-CoV2 is abundant in the lung in fatal coronavirus disease-2019 and is seen primarily in macrophages and endothelial cells; (2) circulating viral capsid proteins (spike, envelope, membrane without RNA) are evident in multiple organs including the skin and brain where it is endocytosed by ACE2+ cells and induce an endothelialitis; (3) both the infectious virus and circulating spike protein induce complement activation and cytologic changes in the viral positive cells.

A Personal Respirator to Improve Protection for Healthcare Workers Treating COVID-19 (PeRSo)

Introduction: SARS-CoV-2 infection is a global pandemic. Personal Protective Equipment (PPE) to protect healthcare workers has been a recurrent challenge in terms of global stocks, supply logistics and suitability. In some settings, around 20% of healthcare workers treating COVID-19 cases have become infected, which leads to staff absence at peaks of the pandemic, and in some cases mortality.

Methods: To address shortcomings in PPE, we developed a simple powered air purifying respirator, made from inexpensive and widely available components. The prototype was designed to minimize manufacturing complexity so that derivative versions could be developed in low resource settings with minor modification.

Results: The “Personal Respirator – Southampton” (PeRSo) delivers High-Efficiency Particulate Air (HEPA) filtered air from a battery powered fan-filter assembly into a lightweight hood with a clear visor that can be comfortably worn for several hours. Validation testing demonstrates that the prototype removes microbes, avoids excessive CO₂ build-up in normal use, and passes fit test protocols widely used to evaluate standard N95/FFP2 and N99/FFP3 face masks. Feedback from doctors and nurses indicate the PeRSo prototype was preferred to standard FFP2 and FFP3 masks, being more comfortable and reducing the time and risk of recurrently changing PPE. Patients report better communication and reassurance as the entire face is visible.

Conclusion: Rapid upscale of production of cheaply produced powered air purifying respirators, designed to achieve regulatory approval in the country of production, could protect healthcare workers from infection and improve healthcare delivery during the COVID-19 pandemic.

SARS-CoV-2: Ultrastructural Characterization of Morphogenesis in an In Vitro System

The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has impacted public health and the world economy and fueled a worldwide race to approve therapeutic and prophylactic agents, but so far there are no specific antiviral drugs. Understanding the biology of the virus is the first step in structuring strategies to combat it, and in this context several studies have been conducted with the aim of understanding the replication mechanism of SARS-CoV-2 in vitro systems. In this work, studies using transmission and scanning electron microscopy and 3D electron microscopy modeling were performed with the goal of characterizing the morphogenesis of SARS-CoV-2 in Vero-E6 cells. Several ultrastructural changes were observed—such as syncytia formation, cytoplasmic membrane projections, lipid droplets accumulation, proliferation of double-membrane vesicles derived from the rough endoplasmic reticulum, and alteration of mitochondria. The entry of the virus into cells occurred through endocytosis. Viral particles were observed attached to the cell membrane and in various cellular compartments, and extrusion of viral progeny took place by exocytosis. These findings allow us to infer that Vero-E6 cells are highly susceptible to SARS-CoV-2 infection as described in the literature and their replication cycle is similar to that described with SARS-CoV and MERS-CoV in vitro models.

Are the northern and southern regions equally affected by the COVID-19 pandemic? An empirical evidence from Nigeria

The new coronavirus infection, being a current global fearful pandemic disease among humans, has spread all over hundreds of countries around the world and has greatly infected millions of people. While the spread of this disease continues among humans, the study aims at determining which part of Nigeria is more affected by coronavirus disease 2019 (COVID-19), as this would assist the national government and other international nongovernmental agencies to plan on the concentration patterns as to which region would require more helping hands in terms of fight against the pandemic disease. Nigeria is stratified into two: southern and northern regions. Data on confirmed cases are sourced from the official website of the Nigeria Centre for Disease Control. These datasets, which cover the periods of February 29 and May 1, 2020 inclusive, are captured on a weekly basis and are grouped according to regional zones, i.e., southern and northern parts. The assumptions of normality and homogeneity of variances are tested via the use of Shapiro-Wilk and Bartlett's statistics. The two tests reveal no violation of any of the assumptions. Thereafter, the t-test is applied with a view to determine the region with a higher chance of being affected by COVID-19. Our results indicate that states in the south have a higher rate of confirmed cases of the pandemic infection than the states in the north. It is therefore concluded that the national government as well as other nongovernmental agencies should focus more on the fight against the pandemic disease in the southern states of Nigeria than in the northern states.

Current challenges in different approaches to control COVID-19: a comprehensive review

BACKGROUND

The World Health Organization declared the outbreak of the novel coronavirus (COVID-19) as a global health emergency on January 30, 2020, and as a pandemic disease on March 11, 2020. This review highlights the international situation, risk factors, and related protections to be taken as prerequisite measures and probable treatment options for the COVID-19-infected population in the current scenario.

MAIN TEXT

The SARS-CoV-2 viruses and their variants caused mild-to-severe respiratory tract infection and used airborne pathways as a way of contagion. Human-to-human transmission led to an exponential growth in the rise in the number of cases making it a real burden to immobilize the rapid spread of the virus while asymptomatic patients created ambiguity for confirmation in the community. It was clear from the case studies of patients that most of them were asymptomatic but still vulnerable to the people around, and hence, in a flash, many countries around the globe went into a complete lockdown, influencing the economy and thrashing industrial outputs. On the other hand, numerous researches were made to counteract the spread through studies in antiviral therapy, immune-based therapy, vaccination development, and natural remedies.

CONCLUSION

Although exploration for a specific drug required for the COVID-19 treatment is under extensive research worldwide and some of them are in clinical trial now. Virtual drug library screening is one of the current techniques for repurposing accessible compounds. This review could provide beneficial information about the potential current and future treatment strategies to treat the pandemic COVID-19 infection.

Mechanisms of SARS-CoV-2 entry into cells

The unprecedented public health and economic impact of the COVID-19 pandemic caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been met with an equally unprecedented scientific response. Much of this response has focused, appropriately, on the mechanisms of SARS-CoV-2 entry into host cells, and in particular the binding of the spike (S) protein to its receptor, angiotensin-converting enzyme 2 (ACE2), and subsequent membrane fusion. This Review provides the structural and cellular foundations for understanding the multistep SARS-CoV-2 entry process, including S protein synthesis, S protein structure, conformational transitions necessary for association of the S protein with ACE2, engagement of the receptor-binding domain of the S protein with ACE2, proteolytic activation of the S protein, endocytosis and membrane fusion. We define the roles of furin-like proteases, transmembrane protease, serine 2 (TMPRSS2) and cathepsin L in these processes, and delineate the features of ACE2 orthologues in reservoir animal species and S protein adaptations that facilitate efficient human transmission. We also examine the utility of vaccines, antibodies and other potential therapeutics targeting SARS-CoV-2 entry mechanisms. Finally, we present key outstanding questions associated with this critical process.

Insight into coronaviruses and natural products-based approach for COVID-19 treatment

There is a deep-rooted belief in mankind that for every illness, somewhere in the world, there exists a botanical-based healing agent in nature in the form of a natural product. Natural products are better equipped to become successful drugs because of their million years of coevolution in a biological milieu. Generally, most herbal formulations and natural products obtained from traditionally used medicinal plants are nontoxic and have rarely shown any adverse side effects on humans. Plants synthesize secondary metabolites primarily for their defense against microbes and herbivores, and because of this, these metabolites have good specificity and potency against harmful pathogens. Nowadays, mankind is facing the contagion effect of SARS-CoV-2 that has caused the ongoing pandemic of COVID-19, which has no specific and effective treatment. Hence this is the time to explore nature for effective, safe, and affordable remedies against this disease. This chapter includes an overview of coronaviruses, their therapeutic targets, and the progress made in identifying lead natural products against the coronaviruses. Additionally, molecular docking and pharmacokinetics analysis of anticoronaviral natural products have been performed to narrow down the possible lead molecules.

Antibodies Produced Toward Recombinant RBD and Nucleocapsid Neutralize SARS-COV-2

Background

The highly contagious SARS-COV-2 virus spread rapidly from China and formed a global pandemic. The virus has infected over 509 million people worldwide and killed about 6.32 million up to date. Up on invasion, the Receptor Binding Domain (RBD) of Spike protein plays a crucial role in the entry of the virus into the host cell. The virus N protein is another protein that has a critical role for genome packaging.

Methods

As bioinformatics approaches, the cassette design, codon adaptation, and protein stability were investigated in this study. Synthetic genes of RBD and N were cloned separately in pET28a + expression vector. They were transferred into Escherichia coli (E. coli) BL21 DE3 host cell, and expression of recombinant proteins was induced with IPTG. The recombinant proteins were purified by column chromatography and approved by Western blotting. Animal immunization was performed with each of the recombinant proteins individually and in combination of the two. The antibody titer of the blood serum from control and immunized mice groups was determined by ELISA technique. Finally, the anti-spike neutralization test was performed.

Results

The expression and purification of RBD protein were monitored on SDS-PAGE, two bands of about 28 and 45 kDa for RBD and N appeared on gel distinctly, which were further validated by Western blotting. According to ELISA results, related antibodies were traced to a dilution of 1/64000 in immunized sera. The neutralization test exhibited produced antibodies' potency to bind the virus proteins. Using SPSS software, statistical analysis was performed by Duncan's test and T-test.

Conclusion

According to the present study, recombinant proteins, either RBD alone or in combination with N adequately stimulated the immune response, and the raised antibodies could neutralize the virus in in vitro test.

Molecular interactions of the M and E integral membrane proteins of SARS-CoV-2

Specific lipid-protein interactions are key for cellular processes, and even more so for the replication of pathogens. The COVID-19 pandemic has drastically changed our lives and caused the death of nearly four million people worldwide, as of this writing. SARS-CoV-2 is the virus that causes the disease and has been at the center of scientific research over the past year. Most of the research on the virus is focused on key players during its initial attack and entry into the cellular host; namely the S protein, its glycan shield, and its interactions with the ACE2 receptors of human cells. As cases continue to rise around the globe, and new mutants are identified, there is an urgent need to understand the mechanisms of this virus during different stages of its life cycle. Here, we consider two integral membrane proteins of SARS-CoV-2 known to be important for viral assembly and infectivity. We have used microsecond-long all-atom molecular dynamics to examine the lipid-protein and protein-protein interactions of the membrane (M) and envelope (E) structural proteins of SARS-CoV-2 in a complex membrane model. We contrast the two proposed protein complexes for each of these proteins, and quantify their effect on their local lipid environment. This ongoing work also aims to provide molecular-level understanding of the mechanisms of action of this virus to possibly aid in the design of novel treatments.