Coronavirus Strain Research Articles

Antigenic features of the strains SARS-CoV-2 of omicron sublines assessed by hyperimmune mouse serum neutralisation

Introduction. The emergence and spread of new genetic variants of SARS-CoV-2 underlies periodic upsurge in COVID-19 incidence. It has been shown that the most rapidly spreading genetic variants of SARS-CoV-2 are resistant to antibodies specific to the previous variant of the SARS-CoV-2, thereby necessitating to analyze the antibody evasion ability of previously circulating variants for newly emerging subvariants. The aim of this work was to assess SARS-CoV-2 cross-reactivity of coronavirus strains belonging to different genetic subvariants of Omicron isolated in the territory of the Russian Federation in the period 2020–2023 in microneutralization reaction using hyperimmune mouse sera. Materials and methods. Mouse hyperimmune sera were obtained against 10 SARS-CoV-2 strains belonging to subvariants BA.1, BA.2, CH.1.1, BN.1, BA.5.1, CL.1.2, BA.5.2, BQ.1.2.1 XBB.1.5 and XBB.3. BALB/c mice were immunized with inactivated concentrated antigen mixed at 1:1 ratio with an adjuvant representing Quillaja saponaria saponin-based virus-like immunostimulatory complex. The antibody titer was determined by neutralization test. The neutralizing activity of the hyperimmune sera was analyzed against the relevant viruses as well as against previous genetic variants of SARS-CoV-2 (Wuhan, Alpha, Beta, Gamma, Delta). Results. Cross-reactivity for all Omicron-variant strains analyzed here was shown; the degree of cross-reactivity depended on the degree of inter-strain relatedness. A prominent cross-reactivity was observed for subvariants of BA.5 so that their neutralizing activity against recombinant SARS-CoV-2 lineages was markedly reduced. Neutralizing serum titers obtained for subvariants of BA.5 against genetic variants of SARS-CoV-2 isolated during the early periods of the pandemic are reduced more than 60-fold. Conclusion. The presented method for obtaining and using hyperimmune mouse sera for neutralization reaction allows the assessment of cross-reactivity for strains belonging to different SARS-CoV-2 subvariants.

BIOTECHNOLOGICAL SYSTEM FOR THE SEARCH OF SUBSTANCES WITH POTENTIAL ACTIVITY AGAINST CORONAVIRUS

Aim. Development of a biotechnological system based on a non-pathogenic coronavirus strain for humans and a sensitive cell line to the selected strain aimed at identifying compounds with potential antiviral activity. Methods. The study was conducted on the cell lines CEF, CEFs, and ВНК-21, which are sensitive to the avian infectious bronchitis virus (IBV). Cell cultivation was performed in flasks and microplates with adhesive surfaces at 37 °C in a 5% CO2 atmosphere. To detach the cells from the growth surface, a Versene solution (0.02%) was used, and for trypsinization of CEF, a trypsin solution (0.25%) was applied. Growth media for all cell cultures were prepared based on a mixture of RPMI-1640 and DMEM in a 1:1 ratio, supplemented with 5% fetal serum. Results. The adaptation of the model virus IBV strain H120 to cultivation in ВНК-21 cell cultures was carried out using intermediate CEF and CEF cultures. In ВНК-21 cells, IBV induced a pronounced cytopathic effect and demonstrated high infectious titers, reaching 5.5 lg TCID50/mL. The use of intermediate CEF and CEF cell cultures facilitated the gradual adaptation of the virus to the new cultivation conditions due to the antigenic affinity between chicken embryo fibroblast cells and avian embryos. Conclusions: As a result of the conducted research, the vaccine virus IBV H-120 was successfully adapted to cultivation conditions in ВНК-21 cell cultures, using primary trypsinized chicken embryo fibroblast cells as an intermediate system. The obtained system "ВНК-21 cell culture + IBV H-120," cultivated at 37 °C in a 5% CO2 atmosphere, can be recommended for use in further biotechnological and virological studies, particularly for evaluating the antiviral activity of potential drugs against coronaviruses.

Genomic characterization and tissue tropism variations of two porcine delta coronavirus strains isolated in China.

The porcine delta coronavirus (PDCoV) is a member of the Delta coronavirus genus, which can lead to diarrhea, vomiting, and mortality in piglets. First detected in Hong Kong in 2012, PDCoV has since spread globally. In January 2024, two strains, CHN-ANHZ-2024 and CHN-JSSQ-2024, were isolated from diarrheal piglets in Anhui and Jiangsu provinces. Immunofluorescence assays, electron microscopy, and genome sequencing were performed. Genome analysis revealed that both PDCoV strains belonged to the Chinese lineage, exhibiting amino acid mutations in the S1 region compared to other strains within the lineage. Amino acid mutation at position 530L is uniquely associated with the Thai strain. Notably, CHN-JSSQ-2024 was identified as a recombinant strain of DH1 and CHN-AHHN-2024, with the recombination occurring in the S2 subunit. CHN-ANHZ-2024 caused severe diarrhea with an 80% mortality rate, whereas CHN-JSSQ-2024 resulted in mild diarrhea without mortality. Viral load analysis showed CHN-ANHZ-2024 primarily infecting the brain and kidneys, while CHN-JSSQ-2024 targeted the lungs, revealing notable differences in tissue tropism. We designed the RNA scope Probe-PDCoV-N to visualize viral RNA in the positively detected organs, viral RNA was detected in the brain, cerebellum, kidneys, and lungs of the infected piglets. This study highlights significant differences in the pathogenicity and organ tropism of two PDCoV strains. The CHN-ANHZ-2024 strain caused severe diarrhea and high mortality in piglets, while the CHN-JSSQ-2024 strain exhibited much milder symptoms. Additionally, the study elucidated notable differences in organ tropism between the strains, offering valuable insights into the epidemiological characteristics and pathogenic mechanisms of PDCoV. These findings provide a foundation for the development of targeted prevention and treatment strategies tailored to specific strains in the future.

A trivalent mucosal vaccine encoding phylogenetically inferred ancestral RBD sequences confers pan-Sarbecovirus protection in mice.

The continued emergence of SARS-CoV-2 variants and the threat of future Sarbecovirus zoonoses have spurred the design of vaccines that can induce broad immunity against multiple coronaviruses. Here, we use computational methods to infer ancestral phylogenetic reconstructions of receptor binding domain (RBD) sequences across multiple Sarbecovirus clades and incorporate them into a multivalent adenoviral-vectored vaccine. Mice immunized with this pan-Sarbecovirus vaccine are protected in the upper and lower respiratory tracts against infection by historical and contemporary SARS-CoV-2 variants, SARS-CoV, and pre-emergent SHC014 and Pangolin/GD coronavirus strains. Using genetic and immunological approaches, we demonstrate that vaccine-induced protection unexpectedly is conferred principally by CD4+ and CD8+ Tcell-mediated anamnestic responses. Importantly, prior mRNA vaccination or SARS-CoV-2 respiratory infection does not alter the efficacy of the mucosally delivered pan-Sarbecovirus vaccine. These data highlight the promise of a phylogenetic approach for antigen and vaccine design against existing and pre-emergent Sarbecoviruses with pandemic potential.

Severity and prognosis of COVID-19 complicated by autoimmune pulmonary alveolar proteinosis

BackgroundThe prognosis of patients with coronavirus disease 2019 (COVID-19) was poor although its survival rate has been improved after the occurrence of the Omicron strain. Autoimmune pulmonary alveolar proteinosis (APAP), a lung disease caused by macrophage dysfunction induced by anti-granulocyte-macrophage colony-stimulating factor (GM–CSF)–neutralizing autoantibodies, is characterized by the deposition of proteinaceous material in the alveolar spaces. The clinical course of COVID-19 in patients with APAP remains unclear and this study aimed to clarify it. MethodsThe data of 23 patients with APAP, who were diagnosed with COVID-19 between January 2020 and May 2023 and collected through a nationwide questionnaire surveillance system, were retrospectively reviewed. ResultsBased on the epidemiological frequency at disease onset, suspected strains of severe acute respiratory syndrome coronavirus 2 were Omicron (n = 18) and non-Omicron (n = 5). Fifteen patients were vaccinated. Six and three patients received anti-viral drugs and corticosteroids, respectively. One patient in the third trimester of pregnancy died despite treatment in the intensive care unit. Six patients were complicated by pneumonia and/or required supplemental oxygen. These patients were suspected to have non-Omicron strains (p = 0.087). Vaccination status showed a significant association with suspected Omicron strains. The radiological findings in four patients and shortness of breath improved in two of the four patients after COVID-19. ConclusionsThe severity and prognosis of the patients were not worse than those predicted based on the results of a previous study. The transition from a non-Omicron strain to an Omicron strain and the vaccination status may have affected these results.

Genomic determinants in pathogenicity of SARS-CoV-2 versa common cold coronaviruses

Determination of the different short oligonucleotide features in the full genome of fatal and mild coronavirus strains can show the researchers how these viruses evolved and became virulent strains. To this aim, at first, in the full genome of all coronavirus strains included in this study, the observed and expected frequency of dinucleotide to hexanucleotide was obtained using Markov method. Then odds ratio (observed/expected abundances) of short oligonucleotide was computed and considered as the raw data (features). Finally, ten distinct weighting algorithms approaches (Information Gain, Information Gain Ratio, Rule, Deviation, Chi Squared, Gini Index, Uncertainty, Relief, Support Vector Machine (SVM), and PCA) was employed on the features to identify oligonucleotide distribution differences across the full genome of SARS-related viruses compared to common cold coronaviruses. Totally among 5440 features (16 dinucleotides, 64 trinucleotides, 256 tetra nucleotides, 1024 penta-nucleotides, and 4096 Hexa-nucleotides), CC, CCA, CCAC, ACCAC, and CACCAC motifs were selected by 80 -90% of all weighting algorithms models to distinguish virulent strains from mild coronaviruses. These remarkable oligonucleotides might point toward the existence of some particular RNA elements that might be involved in viral virulence and thus can be targeted for viral treatment in the future.

An Immunoinformatic Approach for Identifying and Designing Conserved Multi-Epitope Vaccines for Coronaviruses.

The COVID-19 pandemic caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has exposed the vulnerabilities and unpreparedness of the global healthcare system in dealing with emerging zoonoses. In the past two decades, coronaviruses (CoV) have been responsible for three major viral outbreaks, and the likelihood of future outbreaks caused by these viruses is high and nearly inevitable. Therefore, effective prophylactic universal vaccines targeting multiple circulating and emerging coronavirus strains are warranted. This study utilized an immunoinformatic approach to identify evolutionarily conserved CD4+ (HTL) and CD8+ (CTL) T cells, and B-cell epitopes in the coronaviral spike (S) glycoprotein. A total of 132 epitopes were identified, with the majority of them found to be conserved across the bat CoVs, pangolin CoVs, endemic coronaviruses, SARS-CoV-2, and Middle East respiratory syndrome coronavirus (MERS-CoV). Their peptide sequences were then aligned and assembled to identify the overlapping regions. Eventually, two major peptide assemblies were derived based on their promising immune-stimulating properties. In this light, they can serve as lead candidates for universal coronavirus vaccine development, particularly in the search for pan-coronavirus multi-epitope universal vaccines that can confer protection against current and novel coronaviruses.

Comparative profile of the human coronaviruses

The coronavirus disease (COVID-19), a respiratory illness is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is a strain of human corona virus (HCoV) and is infectious in humans. Seven types of human coronaviruses, namely, human coronavirus 229E (HCoV-229E), human coronavirus OC43 (HCoV-OC43), severe acute respiratory syndrome coronavirus SARS-CoV-1, human coronavirus NL63 (HCoV-NL63), human coronavirus HKU1 (HCoV-HKU1), middle east respiratory syndrome-related coronavirus (MERS-CoV) and SARS-CoV-2 have been identified so far. Almost all these viruses spread between people through respiratory droplets produced from coughs or sneezes; the target cells being the epithelial cells of the respiratory tract. In this review, a brief comparative study of these pathogenic CoVs in humans is done which enables an understanding of the evolution in these diseases over a span of almost a century. This review will provide an insight into all HCoVs identified till date.

Multi-Electrode Extended Gate Field Effect Transistors Based on Laser-Induced Graphene for the Detection of Vitamin C and SARS-CoV-2.

Despite the clinical data showing the importance of ascorbic acid (AA or vitamin C) in managing viral respiratory infections, biosensors for their simultaneous detection are lacking. To address this need, we developed a portable and wireless device for simultaneous detection of AA and SARS-CoV-2 virus by integrating commercial transistors with printed laser-induced graphene (LIG) as the extended gate. We studied the effect of laser printing pass number and showed that with two laser printing passes (2-pass LIG), the sensor sensitivity and limit of detection (LOD) for AA improved by a factor of 1.6 and 12.8, respectively. Using complementary characterization methods, we attribute the improved response to a balanced interplay of crystallinity, defect density, surface area, surface roughness, pore density and diameter, and mechanical integrity/stability. These factors enhance analyte transport, reduce noise/variability, and ensure consistent sensor performance, making 2-pass LIG the most effective material in this work. Our sensors exhibit promising performance for detecting AA with a selective response in the presence of common salivary interfering molecules, with sensitivity and LOD of 73.67 mV/dec and 54.04 nM in 1× phosphate buffered saline and 81.05 mV/dec and 78.34 nM in artificial saliva, respectively. We also showed that functionalization of the 2-pass LIG gate with S-protein antibody enables the detection of SARS-CoV-2 protein antigens with an ultralow LOD of 52 zg/mL─an improvement of more than 10-fold compared to 1-pass LIG─and 4 particles/mL for virion mimics with a selective response against influenza virus and multiple human coronavirus strains. With low signal drift/hysteresis and wireless capabilities, the developed device holds great potential for improving at-home monitoring and clinical decision-making.

Design, synthesis, and structure–activity relationships of xanthine derivatives as broad-spectrum inhibitors of coronavirus replication

Illuminated by insights into the hijacking of host cellular metabolism by coronaviruses, we identified an initial hit compound 7030B-C5, characterized by a xanthine scaffold, via a cellular-level phenotypic screening from a domestic repertoire of lipid-modulating agents. A series of derivatives were synthesized and optimized through comprehensive structure–activity relationship (SAR) studies focusing on the N-1, C-8, and N-7 positions of xanthine and preliminary exploration on the N-3 position and parent nucleus. Compounds 10e, 10f and 10o, featuring modifications at the N-7 position, showed inhibitory activity with half maximal effective concentration (EC50) values in the three-digit nanomolar range against human coronavirus-229E (HCoV-229E). In particular, compound 10o exerted superior potency across various coronavirus strains, including HCoV-229E, HCoV-OC43, and the Omicron variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Further investigations revealed that 10o acted on the post-entry stages of virus replication and exhibited a distinctive antiviral mechanism from that of clinically approved nirmatrelvir and molnupiravir. Moreover, drug combination study indicates that 10o operates additively with nirmatrelvir, molnupiravir or omicsynin B4, a dual inhibitor of host proteases for S protein priming. Additionally, in vivo assessments show that 10o has favorable pharmacokinetic and safety profiles compared to its parent compound 7030B-C5. These findings underscore the potential of 10o as a promising antiviral candidate for the treatment of current and potential future coronavirus infections.

Case Report of Benign Diffuse Anterior Scleritis Associated with SARS-CoV-2

COVID-19 is an emerging infectious disease classified as a zoonotic illness caused by the SARS-CoV-2 strain of coronavirus. This enveloped, positive-sense, non-segmented RNA virus belongs to the order Nidovirales and the family Coronaviridae. Its primary mode of transmission is human-to-human through respiratory droplets. Ophthalmologists worldwide have reported various ocular manifestations associated with the infection. Recent studies have shown that SARS-CoV-2 binds to the cellular receptor for angiotensin-converting enzyme 2 (ACE2) and interacts with the transmembrane serine protease 2 (TMPRSS2), both of which are known to be expressed in the human cornea, retina, and conjunctival epithelium [1, 2]. The aim of this work is to present a case of a patient who developed diffuse viral scleritis related to COVID-19, detailing the diagnostic and therapeutic approaches as well as the patient's progression. We report the case of a 63-year-old man with a history of high triglycerides who developed flu-like symptoms and severe tiredness for over a week. A COVID-19 test came back positive. Ten days later, he had a painful, red right eye but no change in vision. An eye exam showed some redness in the conjunctiva, a clear cornea, and normal pressure in the eye. The fellow eye looked normal as well. He was treated with topical steroids and artificial tears, which helped initially. However, after finishing treatment, his symptoms worsened with more redness and pain, and now both eyes were affected. Further examination of the right eye showed swelling of the eyelid (preseptal cellulitis) and widespread redness in the conjunctiva. The Neosynephrine test was negative, and there was pain when moving the eye. The cornea was clear but had some superficial punctate keratitis, and the anterior chamber looked normal. The left eye also showed redness but was otherwise normal. A full lab workup (including blood tests and serologies for HSV1-2) came back normal. Considering his previous C

Modifying the Refuse Chute Design to Prevent Infection Spread: Engineering Analysis and Optimization

Considering the presence of airborne viruses, there is a need for renovation in refuse chutes, regarded as the first step in recycling household waste in buildings. This study aimed to revise the design of existing refuse chutes in light of the challenging experiences in waste management and public health during the coronavirus pandemic. This research primarily focused on the risks posed by various types of coronaviruses, such as the novel coronavirus (COVID-19) and acute respiratory syndrome (SARS and SARS-CoV), on stainless steel surfaces, with evidence of their survival under certain conditions. Refuse chutes are manufactured from stainless steel to resist the corrosive effects of waste. In examining the existing studies, it was observed that Casanova et al. and Chowdhury et al. found that the survival time of coronaviruses on stainless steel surfaces decreases as the temperature increases. Based on these studies, mechanical revisions have been made to the sanitation system of the refuse chute, thus increasing the washing water temperature. Additionally, through mechanical improvements, an automatic solution spray entry is provided before the intake doors are opened. Furthermore, to understand airflow and clarify flow parameters related to airborne infection transmission on residential floors in buildings equipped with refuse chutes, a computational fluid dynamics (CFD) analysis was conducted using a sample three-story refuse chute system. Based on the simulation results, a fan motor was integrated into the system to prevent pathogens from affecting users on other floors through airflow. Thus, airborne pathogens were periodically expelled into the atmosphere via a fan shortly before the intake doors were opened, supported by a PLC unit. Additionally, the intake doors were electronically interlocked, ensuring that all other intake doors remained locked while any single door was in use, thereby ensuring user safety. In a sample refuse chute, numerical calculations were performed to evaluate parameters such as the static suitability of the chute body thickness, static compliance of the chute support dimensions, chute diameter, chute thickness, fan airflow rate, ventilation duct diameter, minimum rock wool thickness for human contact safety, and the required number of spare containers. Additionally, a MATLAB code was developed to facilitate these numerical calculations, with values optimized using the Fmincon function. This allowed for the easy calculation of outputs for the new refuse chute systems and enabled the conversion of existing systems, evaluating compatibility with the new design for cost-effective upgrades. This refuse chute design aims to serve as a resource for readers in case of infection risks and contribute to the literature. The new refuse chute design supports the global circular economy (CE) model by enabling waste disinfection under pandemic conditions and ensuring cleaner source separation and collection for recycling. Due to its adaptability to different pandemic conditions including pathogens beyond coronavirus and potential new virus strains, the designed system is intended to contribute to the global health framework. In addition to the health measures described, this study calls for future research on how evolving global health conditions might impact refuse chute design.

Administration of Lactobacillus plantarum GUANKE alleviates SARS-CoV-2-induced pneumonia in mice.

Most otherwise healthy individuals develop only mild or moderate symptoms of coronavirus disease 2019 (COVID-19) caused by current strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and virus replication is mainly confined to the upper respiratory tract; however, the virus can infect the lower respiratory tract and promote inflammation. Probiotic supplementation has been shown to reduce nasopharyngeal SARS-CoV-2 viral load, reduce the overall number and duration of symptoms, and attenuate inflammation in clinical trials. We showed that a novel L. plantarum GUANKE strain alleviated SARS-CoV-2-induced pneumonia in mice. The transcription and production of inflammatory cytokines were suppressed, and GUANKE moderately reduced the viral load. L. plantarum GUANKE has the potential to become a candidate drug for the treatment of COVID-19 or other viral respiratory infections.

The negative effects of long COVID-19 on cardiovascular health and implications for the presurgical examination.

In 2019, emergence of the novel and communicable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection took scientific communities by surprise and imposed significant burden on healthcare systems globally. Although the advent of this disease piqued the interest of academic centers, healthcare systems, and the general public, there is still much yet to be elucidated regarding epidemiology, pathophysiology, and long-term impacts of coronavirus disease 2019 (COVID-19). It has been established that long COVID-19 can impact multiple organ systems, including the cardiovascular system, unfavorably. Although the pathophysiology of this damage is not well understood, adverse sequelae may range from chest pain and arrhythmias to heart failure (HF), myocardial infarction, or sudden cardiac death. For any postacute COVID-19 patient requiring a surgical procedure, the potential for cardiac injury secondary to long COVID-19 must be considered in the preoperative cardiac examination. This literature review serves to add to the growing body of literature exploring postacute cardiovascular outcomes of COVID-19, with a focus on presurgical cardiac clearance in the adult patient. Specifically, this review studies the prevalence of cardiovascular symptomatology including chest pain, arrhythmias, blood pressure changes, myo-/pericarditis, HF, cardiomyopathy, orthostatic intolerance, and thromboembolism. Although current evidence is scarce in both quality and quantity, it is the goal that this review will highlight the negative impacts of long COVID-19 on cardiovascular health and encourage providers to be cognizant of potential sequelae in the context of the presurgical examination. For this study, peer-reviewed and journal-published articles were selected based on established inclusion and exclusion criteria to address the question "How does long COVID-19 impact the presurgical cardiac examination of an adult scheduled to undergo a noncardiac procedure?" Inclusion criteria included human studies conducted in adult patients and published in peer-reviewed journals up until May 2024 examining the effects of long-COVID-19 infection on the cardiovascular system. Exclusion criteria eliminated unpublished reports, preprints, duplicate articles, literature regarding coronavirus strains other than COVID-19, studies regarding post-COVID-19 vaccination complications, animal studies, and studies conducted in people younger than 18 years of age. A total of 6,675 studies were retrieved from PubMed and Google Scholar. Following screening, 60 studies were included in final consideration. Cardiovascular symptoms of postacute COVID-19 infection were encountered with the following percentages prevalence (total numbers of articles mentioning symptom/total number of articles [60]): chest pain (83.3), arrhythmias (88.3), hypertension (40.0), hypotension (16.7), myocarditis (80.0), pericarditis (51.7), HF (70.0), cardiomyopathy (55.0), orthostatic intolerance (56.7), and thromboembolic events (85.0). The presence of persisting COVID symptoms may negatively impact the patient's physical examination, blood tests, electrocardiogram (ECG), imaging, and/or echocardiogram. Cardiac conditions associated with long COVID require special attention in the context of the presurgical candidate due to an increased risk of sudden cardiac death, myocarditis, stroke, and myocardial infarction- even in those who were healthy prior to acute COVID-19 infection. Until more specific scientific evidence comes to light, care of these patients should be viewed through the prism of the best practices already in use and clinicians should maintain a low threshold to pursue more extensive cardiac workup prior to surgery.

A critical review on phytochemicals as antiviral medications for SARS-CoV-2 virus infection.

A pandemic of acute respiratory infection, which was specified as coronavirus disease 2019, was instigated by a different strain of the virulent coronavirus SARS-CoV-2 that first appeared in late 2019. Since viral infections spread fast and there is presently no effective treatment, the use of plants with a long history of use in treating these infections has been explored regularly. The pandemic of coronavirus disease 2019 (COVID-19) has brought to light the dearth of medications with approval to treat acute viral illnesses. Because of this, the illness had a high fatality rate. The mortality rate was initially quite high and varied according to the patient's geographic location. For instance, among Chinese patients, the rate was 3·6%, whereas 1·5% of COVID-19-related deaths were documented outside of China. As of 2020, India has a 1.4% case fatality rate (CFR) of COVID-19 mortality, compared to 2.8% in Brazil and 1.8% in the USA. Many studies are being conducted to create pharmaceutical compounds specifically targeting important SARS-CoV-2 proteins. Several drug discovery initiatives are being undertaken to find powerful inhibitors by combining biochemical assay and computer-aided drug design techniques. Although plant-derived compounds have not had much success in the dominion of antivirals, plants are, however, believed to be a limitless supply of medications for a variety of diseases and clinical conditions. The scientific foundation required for developing novel natural source medications is provided by the chemical characterization and analysis of plant components. Most viral infections treated by ethnobotanical applications and historical literature on ayurveda, and traditional medicine are generally attributed to phytochemicals, which are compounds derived from medicinal plants. In this review, we have described the application of vascular plant-derived chemicals, such as tannins, polyphenols, alkaloids, and flavonoids, as antivirals, especially for managing COVID-19. This article discusses novel bioactive compounds and their molecular structures that target the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as prospective candidates for anti-coronavirus disease drugs. Moreover, to confirm the effectiveness of the phytochemicals that have demonstrated antiviral activity, clinical trials would need to be conducted in addition to the preclinical research that has already been done. To ensure spectacular findings, more applications of the compound would need to be studied to fully understand the effects of those phytochemicals whose clinical usefulness has already been established.

Towards hybrid approach based SVM and Radiomics features for COVID-19 classification and segmentation

In the battle against the COVID-19 pneumonia outbreak, which is brought on by the coronavirus strain SARS-Cov-2, radiological chest exams, such as chest X-rays, are crucial. In order to understand the unique radiographic characteristics of COVID-19, this research looks into classification models to distinguish chest X-ray images based on Radiomics features. This study is performed with datasets composed of 136 segmented chest X-rays, which were used to train and test the categorization algorithms. First and second-order statistical texture characteristics were extracted from the right (R), left (L), superior, middle, and bottom lung zones for each lung side using the Pyradiomics collection. Data was divided into training (80%) and test (20%) groups for feature selection. After assessing the respective feature significance and confirmation accuracy, the most pertinent Radiomics features were chosen. A model of lung segmentation based grey level pixels was used to evaluate support vector machines (SVM) as possible classifiers (AUC = 83.7%). Our research reveals a preference for the upper lung zone and a preponderance of Radiomics feature selection in the right lung. Our future research will concentrate on COVID-19 categorization and segmentation for more precise forecast using a hybrid method based on SVM and Radiogenomics features.

In silico investigation of HCV and RNA synthesis inhibitor antibiotic drugs as potential inhibitors of SARS‑CoV‑2 main protease (Mpro)

BackgroundSince December 2019, a global crisis has unfolded with the emergence of a new strain of coronavirus known as SARS-CoV-2. This pandemic has afflicted hundreds of millions of people worldwide, resulting in millions of fatalities. In response to this urgent healthcare crisis, extensive efforts have been made to discover inhibitors of the COVID-19 virus. Given the structural similarities between SARS-CoV-2 and HCV, drugs approved by the FDA for treating HCV were selected and subjected to in silico testing against the SARS-CoV-2 virus, with Remdesivir used as the standard for validation. Drug repurposing and phytochemical testing have also been conducted to identify potential candidates capable of inhibiting or suppressing the infection caused by the coronavirus. The time constraints imposed by the pandemic necessitated the in silico analysis of existing drug molecules against the coronavirus. Eleven HCV drugs approved by the FDA, along with one RNA synthesis inhibitor antibiotic drug, were tested using the in silico method due to their structural similarities with HCV and the SARS-CoV-2 virus.ResultsMolecular docking and MD simulation studies were performed for all selected compounds. Binding energies, root-mean-square deviation, root-mean-square fluctuation, solvent-accessible surface area, radius of gyration, and molecular mechanics generalized born surface area were calculated. Based on docking and MD simulation studies all the selected compounds have shown good binding energy values with Mpro (PDB ID: 6LU7). No toxicity measurements are required for these drugs since they were previously tested prior to their approval by the FDA.ConclusionsThis study shows that FDA-approved HCV drugs can be used as for SARS-COVID-19 inhibitors.

A Comparison between Demyelinating and Omicron Variant Infection-Associated Optic Neuritis.

The connection between viral infection and the onset of demyelination has garnered considerable attention. Omicron, the most recent prevalent strain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has raised concerns. Optic neuritis (ON) associated with Omicron infection and spontaneous demyelinating ON may manifest distinct disease progressions. This study aims to contrast the features of these two distinct etiologies of ON. This case-control study comprised fifteen patients (21 eyes) diagnosed with Omicron infection-related ON and fifteen patients (24 eyes) with demyelinating ON serving as the control group. Clinical characteristics, cerebrospinal fluid (CSF) analysis, treatment protocols, and outcomes were compared between the two groups. The Omicron-infected group exhibited a higher incidence of pain upon ocular movement (p = 0.023) and peripapillary hemorrhages (p = 0.046). In CSF analysis, there was an elevation in white cell counts (WCCs) (p = 0.004), with lymphocytes being the predominant cell type in the Omicron-related ON group. However, oligoclonal bands (OCBs), indicative of intrathecal synthesis, were significantly lower and lagged behind those of the demyelinating ON group (p = 0.021). SARS-CoV-2 RNA was not directly detected in the CSF of the Omicron-related ON group, and the degree of WCC elevation was closely linked with peripapillary hemorrhages (odds ratio = 0.029, p = 0.02). Additionally, the Omicron-related ON group displayed more pronounced ganglion cell loss following 3-month treatment (p = 0.02). Omicron-related ON is distinguished by more pronounced clinical symptoms and distinct CSF characteristics compared to spontaneous demyelinating ON. The absence of viral RNA sequence in the CSF of Omicron-associated ON supports the use of steroid monotherapy; however, varying treatment options and prognoses should be considered for these two types of ON.

Association of COVID with Mycosis in General.

The COVID-19 pandemic caused by SARS-CoV-2 is a respiratory disease which created havoc worldwide, was accompanied by another peculiar, otherwise rare, secondary fungal infection Mucormycosis which was observed at exceptionally high incidence in India during the second wave of COVID-19. The article explores possible links between the two infectious diseases to understand a higher-than-normal occurrence of Mucormycosis in COVID-19 patients. Coronavirus enters the patients through ACE-2 and many other receptors like- NRP-1, TfR, CD-126, and CD-26. Virus bind to cells possessing these receptors and affect their proper functioning, disturbing homeostatic metabolism and resulting in conditions like hyperglycemia, Diabetic Ketoacidosis (DKA), low serum pH, iron overload, anemia, hypoxia, and immunosuppression as explained in the article. All these outcomes provide a very supportive environment for the attack and spread of Mucormycosis fungi. The major receptor for Mucormycosis in humans is the GRP-78. Its expression is upregulated by coronavirus entry and by hyperferritinemia, hyperglycemia, and acidic conditions prevalent in COVID patients, thus providing an easy entry for the fungal species. Upregulation of GRP-78 furthermore damages pancreatic β-cells and intensifies hyperglycemia, showing quite a synergic relationship. Inordinate rise of Mucormycosis cases in India might be explained by facts like- India possessing a large proportion of diabetic patients, emergence of a very deadly strain of coronavirus- Delta strain, higher doses of steroids and antibodies used to treat patients against this strain, overburdened health care services, sudden much higher need of oxygen supply and use of industrial oxygen could explain the Mucormycosis outbreak observed in India during the second wave of COVID-19. The present review discusses the functional interdependence between COVID-19 and Mucormycosis and summarizes the possible synergic links between COVID and Mucormycosis. The receptors and metabolic pathways affected by COVID-19 result in severe physiological conditions- hyperglycemia, DKA, anemia, iron overload, immunosuppression, and hypoxia. All these conditions not only increase the expression of GRP-78, the major receptor for entry of fungi but also play a crucial role in providing quality media for Mucormycosis fungus to establish and grow. Hence explains the fungal epidemic observed in India during the second wave of COVID-19 in India.

The Association between Comorbidity and Severity of SARS-CoV-2 Omicron Variant (B.1.1.529) Infection in Bengkulu: A Cross-Sectional Study

Introduction: The Omicron variant is a strain of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) with higher infectivity and transmissibility (2.8 and 3.2 times) than Delta, but the pathogenicity of Omicron is weaker. Some studies indicate that a history of comorbidities can enhance the pathogenicity. Objectives: This research investigates the correlation between comorbidity and disease severity in COVID-19 patients with the Omicron variant in Bengkulu. Methods: This observational type with cross-sectional design consisted of 191 COVID-19 patients from January to December 2022. COVID-19 positive confirmation was collected through RT-PCR and medical records from Dr. M. Yunus, Harapan dan Doa, and Rafflesia Hospital with total sampling method. The medical record encompassed demographic characteristics, clinical manifestation features, and comorbid types. Subsequently, an analysis was conducted to examine the correlation between comorbidity and disease severity using the Spearman Rank test. Results: The majority of subjects were 18-60 years (60.7%) and 53.9% were male. Most of the subjects experienced cough (72,7%) and were at a moderate level (47.6%). The most common comorbid were hypertension (21.3%), and cardiovascular diseases (20.6%), and the third common comorbid were diabetes and chronic kidney disease (15.4%). Overall, the disease severity was observed in 58 patients with mild, 91 moderate, and 42 severe. Spearman Rank test showed a significant correlation (p = 0,000) between comorbidities and disease severity of COVID-19 patients with the Omicron variant in Bengkulu City with moderate correlation strength (rs = 0,572). Conclusions: The comorbidity history significantly influences the severity of illness among COVID-19 Omicron variant patients, whereby an increased number of comorbidities aggravated the severity of the disease.