Coronavirus pathogenesis

GCN2 in Viral Defence and the Subversive Tactics Employed by Viruses

The recent SARS-CoV-2 pandemic and associated COVID19 disease illustrates the important role of viral defence mechanisms in ensuring survival and recovery of the host or patient. Viruses absolutely depend on the host's protein synthesis machinery to replicate, meaning that impeding translation is a powerful way to counteract viruses. One major approach used by cells to obstruct protein synthesis is to phosphorylate the alpha subunit of eukaryotic translation initiation factor 2 (eIF2α). Mammals possess four different eIF2α-kinases: PKR, HRI, PEK/PERK, and GCN2. While PKR is currently considered the principal eIF2α-kinase involved in viral defence, the other eIF2α-kinases have also been found to play significant roles. Unsurprisingly, viruses have developed mechanisms to counteract the actions of eIF2α-kinases, or even to exploit them to their benefit. While some of these virulence factors are specific to one eIF2α-kinase, such as GCN2, others target all eIF2α-kinases. This review critically evaluates the current knowledge of viral mechanisms targeting the eIF2α-kinase GCN2. A detailed and in-depth understanding of the molecular mechanisms by which viruses evade host defence mechanisms will help to inform the development of powerful anti-viral measures.

Efficiency of hospitals in COVID-19 era: a case study of an affected country

BACKGROUND

The COVID-19 pandemic has affected all aspects of human life and society and has damaged the global economy. Health systems and hospitals were not exempted from this situation. The performance of hospitals during the COVID-19 pandemic was affected by policies related to the pandemic and other factors. This study aimed to investigate hospital performance indicators such as admissions and revenue.

METHODS

The medical records of patients with selected orthopedic and general surgical diseases were studied in two government hospitals in the capital city of Urmia in the second quarter of 2019, with the same period in 2020. Data were extracted based on the number of medical records, including length of stay, hospitalization type, sex, age, insurance, number of deaths, and readmissions from the medical records department. Payment amounts were collected from the revenue department and Hospital Information System. Two performance indicators, two result indicators, and two control indicators were used. Mean disease-specific revenue, total revenue, length of stay, and bed occupancy rate were calculated for both periods. Data were analyzed using SPSS (version 16) and the Mann-Whitney statistical test.

RESULTS

2140 cases were studied in the two disease groups. An increase was observed in the number of hospitalizations and average length of stay during the pandemic. The mean disease-specific revenue in the quarter of 2020 was higher than in 2019. However, total revenue decreased, and the difference in the mean of total revenue was significant for the two years (P = 0.00) in teaching center. The number of readmissions remained unchanged throughout in the pandemic. The number of deaths due to general surgery diseases in 2020 compared to the same period in 2019 was associated with a relative increase.

CONCLUSIONS

The COVID-19 pandemic increased the slope of health care costs. The analysis of the studied variables as performance, result, and control indicators showed that hospitalization rate, bed occupancy rate, and total revenue followed a similar and decreasing pattern in the selected hospitals during the COVID-19 pandemic. Hospitals should adopt appropriate strategies so that, in conditions identical to the COVID-19 pandemic, their performance is accompanied by proper management of resources, efficiency, and minimal reduction in revenue.

Analysis of the expression of the Serpina1 gene in SARS-CoV-2 infection: study of a new biomarker

INTRODUCTION

The SERPINA1 gene encodes the protein Alpha-1 Antitrypsin (AAT1). Possible imbalances between the concentrations of proteases and antiproteases (AAT1) can lead to the development of serious pulmonary and extrapulmonary pathologies. In this work we study the importance of this possible imbalance in patients with COVID-19.

OBJECTIVES

To correlate the severity of the symptoms of SARS-COV-2 infection with the AAT1 concentrations at diagnosis of the disease.

METHODS

An observational, prospective, cross-sectional, non-interventional, analytical study was carried out where 181 cases with COVID-19 admitted to the "Lozano Blesa" University Clinical Hospital of Zaragoza were selected. The concentration of AAT1 was studied in all of them and this was correlated with the clinical aspects and biochemical parameters at hospital admission.

RESULTS

141 cases corresponded to patients with severe COVID and 40 patients with mild COVID. AAT1 levels were positively correlated with the days of hospitalization, severity, C-Reactive Protein, ferritin, admission to Intensive Care, and death, and presented a negative correlation with the number of lymphocytes/mm3. AAT1 concentrations higher than 237.5 mg/dL allowed the patient to be classified as "severe" (S72%; E78%) and 311.5 mg/dL were associated with the risk of admission to Intensive Care or Exitus (S67%; E79%).

CONCLUSIONS

Levels of the SERPINA1 gene expression product, AAT1, correlate with the severity of COVID-19 patients at diagnosis of the disease, being useful as a prognostic biomarker.

SARS-CoV-2 Omicron BA.1 Variant Infection of Human Colon Epithelial Cells

The Omicron variant of SARS-CoV-2, characterized by multiple subvariants including BA.1, XBB.1.5, EG.5, and JN.1, became the predominant strain in early 2022. Studies indicate that Omicron replicates less efficiently in lung tissue compared to the ancestral strain. However, the infectivity of Omicron in the gastrointestinal tract is not fully defined, despite the fact that 70% of COVID-19 patients experience digestive disease symptoms. Here, using primary human colonoids, we found that, regardless of individual variability, Omicron infects colon cells similarly or less effectively than the ancestral strain or the Delta variant. The variant induced limited type III interferon expression and showed no significant impact on epithelial integrity. Further experiments revealed inefficient cell-to-cell spread and spike protein cleavage in the Omicron spike protein, possibly contributing to its lower infectious particle levels. The findings highlight the variant-specific replication differences in human colonoids, providing insights into the enteric tropism of Omicron and its relevance to long COVID symptoms.

Machine Learning to Identify Critical Biomarker Profiles in New SARS-CoV-2 Variants

The global dissemination of SARS-CoV-2 resulted in the emergence of several variants, including Alpha, Alpha + E484K, Beta, and Omicron. Our research integrated the study of eukaryotic translation factors and fundamental components in general protein synthesis with the analysis of SARS-CoV-2 variants and vaccination status. Utilizing statistical methods, we successfully differentiated between variants in infected individuals and, to a lesser extent, between vaccinated and non-vaccinated infected individuals, relying on the expression profiles of translation factors. Additionally, our investigation identified common causal relationships among the translation factors, shedding light on the interplay between SARS-CoV-2 variants and the host's translation machinery.

COVID-19 Associated Cardiovascular Disease-Risks, Prevention and Management: Heart at Risk Due to COVID-19

The SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) virus and the resulting COVID-19 pandemic have had devastating and lasting impact on the global population. Although the main target of the disease is the respiratory tract, clinical outcomes, and research have also shown significant effects of infection on other organ systems. Of interest in this review is the effect of the virus on the cardiovascular system. Complications, including hyperinflammatory syndrome, myocarditis, and cardiac failure, have been documented in the context of COVID-19 infection. These complications ultimately contribute to worse patient outcomes, especially in patients with pre-existing conditions such as hypertension, diabetes, or cardiovascular disease (CVD). Importantly and interestingly, reports have demonstrated that COVID-19 also causes myocardial injury in adults without pre-existing conditions and contributes to systemic complications in pediatric populations, such as the development of multisystem inflammatory syndrome in children (MIS-C). Although there is still a debate over the exact mechanisms by which such complications arise, understanding the potential paths by which the virus can influence the cardiovascular system to create an inflammatory environment may clarify how SARS-CoV-2 interacts with human physiology. In addition to describing the mechanisms of disease propagation and patient presentation, this review discusses the diagnostic findings and treatment strategies and the evolution of management for patients presenting with cardiovascular complications, focusing on disease treatment and prevention.

Serpentoviruses Exhibit Diverse Organization and ORF Composition with Evidence of Recombination

Serpentoviruses are a subfamily of positive sense RNA viruses in the order Nidovirales, family Tobaniviridae, associated with respiratory disease in multiple clades of reptiles. While the broadest viral diversity is reported from captive pythons, other reptiles, including colubrid snakes, turtles, and lizards of captive and free-ranging origin are also known hosts. To better define serpentoviral diversity, eleven novel serpentovirus genomes were sequenced with an Illumina MiSeq and, when necessary, completed with other Sanger sequencing methods. The novel serpentoviral genomes, along with 57 other previously published serpentovirus genomes, were analyzed alongside four outgroup genomes. Genomic analyses included identifying unique genome templates for each serpentovirus clade, as well as analysis of coded protein composition, potential protein function, protein glycosylation sites, differences in phylogenetic history between open-reading frames, and recombination. Serpentoviral genomes contained diverse protein compositions. In addition to the fundamental structural spike, matrix, and nucleoprotein proteins required for virion formation, serpentovirus genomes also included 20 previously uncharacterized proteins. The uncharacterized proteins were homologous to a number of previously characterized proteins, including enzymes, transcription factors, scaffolding, viral resistance, and apoptosis-related proteins. Evidence for recombination was detected in multiple instances in genomes from both captive and free-ranging snakes. These results show serpentovirus as a diverse clade of viruses with genomes that code for a wide diversity of proteins potentially enhanced by recombination events.

Neurons cytoskeletal architecture remodeling during the replication cycle of mouse coronavirus MHV-JHM: a morphological in vitro study

Nowadays, the population is still struggling with a post-COVID19 syndrome known as long COVID, including a broad spectrum of neurological problems. There is an urgent need for a better understanding and exploration of the mechanisms of coronavirus neurotropism. For this purpose, the neurotropic strain of mouse hepatitis virus (MHV-JHM) originating from the beta-coronavirus genus, the same as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been used. The role of the cytoskeleton during virus replication in neurons in vitro was determined to understand the mechanisms of MHV-JHM neuroinfection. We have described for the first time the changes of actin filaments during MHV-JHM infection. We also observed productive replication of MHV-JHM in neurons during 168 h p.i. and syncytial cytopathic effect. We discovered that the MHV-JHM strain modulated neuronal cytoskeleton during infection, which were manifested by: (i) condensation of actin filaments in the cortical layer of the cytoplasm, (ii) formation of microtubule cisternae structures containing viral antigen targeting viral replication site (iii) formation of tunneling nanotubes used by MHV-JHM for intercellular transport. Additionally, we demonstrated that the use of cytoskeletal inhibitors have reduced virus replication in neurons, especially noscapine and nocodazole, the microtubule shortening factors.

Analysis of the clinical characteristics in 18 patients with novel coronavirus pneumonia: Observational study

The aim of the present study was to analyze the clinical features, treatments, and short-term prognoses of 18 patients with novel coronavirus pneumonia (NCP) in order to provide reference for further clinical prevention and control of the epidemic. From January 29 to February 29, 2020, data from 18 patients with NCP who were positive for the 2019 novel coronavirus nucleic acid test were collected, and their clinical manifestations, laboratory tests, imaging features, and treatment protocols were analyzed retrospectively. From among the 18 patients with NCP, 9 (50%) were imported cases and 9 (50%) had contact histories with confirmed adult patients. Clinical classification was mainly of the normal type (16 cases, 88.9%). Fever and cough were common clinical symptoms, and the main laboratory indices were lymphocytopenia and leukocytopenia. The main imaging findings yielded ground-glass opacity in 12 cases (66.7%) and patchy opacity in 9 cases (50%). All 18 patients were treated with antiviral therapy and targeted treatment in accordance with their symptoms, returned negative nucleic acid tests (9-23 days) after their treatment, and were cured and discharged by March 5, 2020. During the early stages in Deyang, most patients with NCP were input cases; in the later stages, the main route of infection was close contact within the family. Close contact history in epidemiology, nucleic acid detection, and chest imaging were important references for diagnosis. Antiviral therapy resulted in good therapeutic effects. Adopting multi-departmental consultation and remote consultation in combination with traditional Chinese medicine treatment and psychological counseling may result in a good short-term prognosis.

The pleiotropic approach to coronavirus disease-19 pathogenesis: The impact of liver diseases associated host genetic variants

Coronavirus disease-2019 (COVID-19) is a novel multisystemic viral disease caused pandemic. The disease impact involves liver and associated systems. Undoubtedly, host genetic background influences the predisposition and prediction of infection. Variants among human populations might increase susceptibility or protect against severe outcomes. In this manner, rs738409 variant of patatin-like phospholipase domain-containing protein 3 gene appears to be protective in some populations in spite of its aggravating effect on non-alcoholic fatty liver diseases (NAFLDs) and steatohepatitis. DRB1*15:01 allele of human leukocyte antigen is associated with protective effect in European and Japanese populations. DRB1*03:01 contrarily increases the susceptibility of severe COVID-19 infection in European populations. rs1260326 in glucokinase regulatory protein gene, rs112875651 in tribbles homolog 1 gene, rs429358 in apolipoprotein 1, and rs58542926 in transmembrane 6 superfamily 2 alleles are found related with NAFLD and obesity; thus, hypercoagulability and severe COVID-19 outcomes. In chronic or acute liver diseases, comorbid syndromes are the key factors to explain increased severity. There might not be a direct association between the variant and severe COVID-19 infection. As it is concluded, there are genes and variants known and unknown yet to be studied to reveal the association with disease severity.

In silico drug repurposing carvedilol and its metabolites against SARS-CoV-2 infection using molecular docking and molecular dynamic simulation approaches

The pandemic of coronavirus disease 2019 (COVID-19) caused by the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a significant impact on the economy and public health worldwide. Therapeutic options such as drugs and vaccines for this newly emerged disease are eagerly desired due to the high mortality. Using the U.S. Food and Drug Administration (FDA) approved drugs to treat a new disease or entirely different diseases, in terms of drug repurposing, minimizes the time and cost of drug development compared to the de novo design of a new drug. Drug repurposing also has some other advantages such as reducing safety evaluation to accelerate drug application on time. Carvedilol, a non-selective beta-adrenergic blocker originally designed to treat high blood pressure and manage heart disease, has been shown to impact SARS-CoV-2 infection in clinical observation and basic studies. Here, we applied computer-aided approaches to investigate the possibility of repurposing carvedilol to combat SARS-CoV-2 infection. The molecular mechanisms and potential molecular targets of carvedilol were identified by evaluating the interactions of carvedilol with viral proteins. Additionally, the binding affinities of in vivo metabolites of carvedilol with selected targets were evaluated. The docking scores for carvedilol and its metabolites with RdRp were - 10.0 kcal/mol, - 9.8 kcal/mol (1-hydroxyl carvedilol), - 9.7 kcal/mol (3-hydroxyl carvedilol), - 9.8 kcal/mol (4-hydroxyl carvedilol), - 9.7 kcal/mol (5-hydroxyl carvedilol), - 10.0 kcal/mol (8-hydroxyl carvedilol), and - 10.1 kcal/mol (O-desmethyl carvedilol), respectively. Using the molecular dynamics simulation (100 ns) method, we further confirmed the stability of formed complexes of RNA-dependent RNA polymerase (RdRp) and carvedilol or its metabolites. Finally, the drug-target interaction mechanisms that contribute to the complex were investigated. Overall, this study provides the molecular targets and mechanisms of carvedilol and its metabolites as repurposed drugs to fight against SARS-CoV-2 infection.

Role of Metals on SARS-CoV-2 Infection: a Review of Recent Epidemiological Studies

PURPOSE OF REVIEW

Metals and metalloids are known for their nutritional as well as toxic effects in humans. In the context of the SARS-CoV-2 pandemic, understanding the role of metals on COVID-19 infection is becoming important due to their role in infectious diseases. During the past 2 years, a significant number of studies have examined the impact of metals and metalloids on COVID-19 morbidity and mortality. We conducted a systematic review of peer-reviewed manuscripts on the association of metals and metalloids with SARS-CoV-2 infection and COVID-19 severity published since the onset of the pandemic.

RECENT FINDINGS

We searched for epidemiological studies available through the PubMed database published from January 2020 to December 2022. Of 92 studies identified, 20 met our inclusion criteria. These articles investigated the association of zinc (Zn), iron (Fe), selenium (Se), manganese (Mn), cadmium (Cd), arsenic (As), copper (Cu), magnesium (Mg), chromium (Cr), and/or lead (Pb) levels on SARS-CoV-2 infection and/or COVID-19 severity. Of the ten metals and metalloids of interest that reported either positive, negative, or no associations, Zn yielded the highest number of articles (n = 13), followed by epidemiological studies on Se (n = 7) and Fe (n = 5). Elevated serum Zn and Se were associated with reduced COVID-19 severity and mortality. Similarly, higher levels of serum Fe were associated with lower levels of cellular damage and symptoms of SARS-CoV-2 infection and with faster recovery from COVID-19. On the other hand, higher serum and urinary Cu and serum Mg levels were associated with higher COVID-19 severity and mortality. Along with the positive or negative effects, some studies reported no impact of metals on SARS-CoV-2 infection. This systematic review suggests that metals, particularly Zn, Fe, and Se, may help reduce the severity of COVID-19, while Cu and Mg may aggravate it. Our review suggests that future pandemic mitigation strategies may evaluate the role of Zn, Se, and Fe as potential therapeutic interventions.

Novel pseudonucleosides and sulfamoyl-oxazolidinone β-D-glucosamine derivative as anti-COVID-19: design, synthesis, and in silico study

New pseudonucleosides containing cyclic sulfamide moiety and sulfamoyl β-D-glucosamine derivative are described. These pseudonucleosides are synthesized in good yields starting from chlorosulfonyl isocyanate and β-D-glucosamine hydrochloride in five steps; (protection, acetylation, removal of the Boc group, sulfamoylation, and cyclization). Further, novel glycosylated sulfamoyloxazolidin-2-one is prepared in three steps; carbamoylation, sulfamoylation, and intramolecular cyclization. The structures of the synthesized compounds were confirmed by usual spectroscopic and spectrometric methods NMR, IR, MS, and EA. Interesting molecular docking of the prepared pseudonucleosides and (Beclabuvir, Remdesivir) drugs with SARS-CoV-2/Mpro (PDB:5R80) was conducted using the same parameters for a fair comparison. A low binding affinity of the synthesized compounds compared to the Beclabuvir and other analysis showed that pseudonucleosides have the ability to inhibit SARS-CoV-2. After the motivating results of molecular docking study, the complex between the SARS-CoV-2 Mpro and compound 7 was subjected to 100 ns molecular dynamics (MD) simulation using Desmond module of Schrodinger suite, during which the receptor-ligand complex showed substantial stability after 10 ns of MD simulation. Also, we studied the prediction of absorption, distribution, properties of metabolism, excretion, and toxicity (ADMET) of the synthesized compounds.Communicated by Ramaswamy H. Sarma.

Separation and quantification of Azvudine in plasma of patients with COVID-19 using LC-MS/MS

Azvudine (FNC) is a new drug conditionally approved in 2022 for the treatment of coronavirus disease 2019 (COVID-19) in China. However, the exposure level of FNC in COVID-19 patients in clinical practice is still obscure, and there is no liquid chromatography-tandem mass spectrometry (LC-MS/MS) or LC method reported for quantifying the FNC. In this study, a simple, fast, and reliable LC-MS/MS method using L-phenylalanine-D5 (Phe-D5) as the internal standard (IS) was developed for the quantification of FNC in plasma from COVID-19 patients. After simple protein precipitation with methanol, the analyte in the supernatant was separated on Waters Atlantis® T3 (2.1 ×100 mm, 3.0 µm) column with the mobile phase consisting of acetonitrile (ACN) - aqueous solution (containing 0.03% heptafluorobutyric acid and 0.2% formic acid). The mobile phase was delivered at 0.3 mL/min in an isocratic elution program (15:85, V: V). The linear relationship of FNC was good within the calibration range of 2.0 - 2000.0 ng/mL, with the recovery of FNC ranging from 81.37% to 103.31% and the matrix effect was 94.77%- 109.83%. The short-term, long-term, and freeze-thaw stability of the FNC assessed in method was acceptable, and all other items met the requirements of validation of the biological analytical method. Finally, the method was applied to detect the exposure level of FNC in plasma samples from patients diagnosed with COVID-19, and the results, which are within the linear range of the method, showed huge inter-individual variation, supporting the significance of therapeutic drug monitoring of FNC.

A novel recombinant S-based subunit vaccine induces protective immunity against porcine deltacoronavirus challenge in piglets

IMPORTANCE

As an emerging porcine enteropathogenic coronavirus that has the potential to infect humans, porcine deltacoronavirus (PDCoV) is receiving increasing attention. However, no effective commercially available vaccines against this virus are available. In this work, we designed a spike (S) protein and receptor-binding domain (RBD) trimer as a candidate PDCoV subunit vaccine. We demonstrated that S protein induced more robust humoral and cellular immune responses than the RBD trimer in mice. Furthermore, the protective efficacy of the S protein was compared with that of inactivated PDCoV vaccines in piglets and sows. Of note, the immunized piglets and suckling pig showed a high level of NAbs and were associated with reduced virus shedding and mild diarrhea, and the high level of NAbs was maintained for at least 4 months. Importantly, we demonstrated that S protein-based subunit vaccines conferred significant protection against PDCoV infection.

A suitable model to investigate acute neurological consequences of coronavirus infection

OBJECTIVE AND DESIGN

The present study aimed to investigate the neurochemical and behavioral effects of the acute consequences after coronavirus infection through a murine model.

MATERIAL

Wild-type C57BL/6 mice were infected intranasally (i.n) with the murine coronavirus 3 (MHV-3).

METHODS

Mice underwent behavioral tests. Euthanasia was performed on the fifth day after infection (5 dpi), and the brain tissue was subjected to plaque assays for viral titration, ELISA, histopathological, immunohistochemical and synaptosome analysis.

RESULTS

Increased viral titers and mild histological changes, including signs of neuronal degeneration, were observed in the cerebral cortex of infected mice. Importantly, MHV-3 infection induced an increase in cortical levels of glutamate and calcium, which is indicative of excitotoxicity, as well as increased levels of pro-inflammatory cytokines (IL-6, IFN-γ) and reduced levels of neuroprotective mediators (BDNF and CX3CL1) in the mice brain. Finally, behavioral analysis showed impaired motor, anhedonia-like and anxiety-like behaviors in animals infected with MHV-3.

CONCLUSIONS

In conclusion, the data presented emulate many aspects of the acute neurological outcomes seen in patients with COVID-19. Therefore, this model may provide a preclinical platform to study acute neurological sequelae induced by coronavirus infection and test possible therapies.

An Overview of SARS-CoV-2 Etiopathogenesis and Recent Developments in COVID-19 Vaccines

The Coronavirus disease-2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has significantly impacted the health and socioeconomic status of humans worldwide. Pulmonary infection of SARS-CoV-2 results in exorbitant viral replication and associated onset of inflammatory cytokine storm and disease pathology in various internal organs. However, the etiopathogenesis of SARS-CoV-2 infection is not fully understood. Currently, there are no targeted therapies available to cure COVID-19, and most patients are treated empirically with anti-inflammatory and/or anti-viral drugs, based on the disease symptoms. Although several types of vaccines are currently implemented to control COVID-19 and prevent viral dissemination, the emergence of new variants of SARS-CoV-2 that can evade the vaccine-induced protective immunity poses challenges to current vaccination strategies and highlights the necessity to develop better and improved vaccines. In this review, we summarize the etiopathogenesis of SARS-CoV-2 and elaborately discuss various types of vaccines and vaccination strategies, focusing on those vaccines that are currently in use worldwide to combat COVID-19 or in various stages of clinical development to use in humans.

Neuromuscular defects after infection with a beta coronavirus in mice

COVID-19 affects primarily the lung. However, several other systemic alterations, including muscle weakness, fatigue and myalgia have been reported and may contribute to the disease outcome. We hypothesize that changes in the neuromuscular system may contribute to the latter symptoms observed in COVID-19 patients. Here, we showed that C57BL/6J mice inoculated intranasally with the murine betacoronavirus hepatitis coronavirus 3 (MHV-3), a model for studying COVID-19 in BSL-2 conditions that emulates severe COVID-19, developed robust motor alterations in muscle strength and locomotor activity. The latter changes were accompanied by degeneration and loss of motoneurons that were associated with the presence of virus-like particles inside the motoneuron. At the neuromuscular junction level, there were signs of atrophy and fragmentation in synaptic elements of MHV-3-infected mice. Furthermore, there was muscle atrophy and fiber type switch with alteration in myokines levels in muscles of MHV-3-infected mice. Collectively, our results show that acute infection with a betacoronavirus leads to robust motor impairment accompanied by neuromuscular system alteration.

History, origin, transmission, genome structure, replication, epidemiology, pathogenesis, clinical features, diagnosis, and treatment of COVID-19: A review

In December, 2019, pneumonia triggered by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surfaced in Wuhan, China. An acute respiratory illness named coronavirus disease 2019 (COVID-19) is caused by a new coronavirus designated as SARS-CoV-2. COVID-19 has surfaced as a major pandemic in the 21st century as yet. The entire world has been affected by this virus. World Health Organization proclaimed COVID-19 pandemic as a public health emergency of international concern on January 30, 2020. SARS-CoV-2 shares the same genome as coronavirus seen in bats. Therefore, bats might be its natural host of this virus. It primarily disseminates by means of the respiratory passage. Evidence revealed human-to-human transmission. Fever, cough, tiredness, and gastrointestinal illness are the manifestations in COVID-19-infected persons. Senior citizens are more vulnerable to infections which can lead to dangerous consequences. Various treatment strategies including antiviral therapies are accessible for the handling of this disease. In this review, we organized the most recent findings on COVID-19 history, origin, transmission, genome structure, replication, epidemiology, pathogenesis, clinical features, diagnosis, and treatment strategies.

Acute thrombotic occlusion involving three coronary arteries. A unique association with COVID-19 pneumonia

Key Clinical Message

Respiratory viruses, particularly COVID-19, can be associated with severe cases of myocardial infarction (MI). Physicians should have a low threshold for MI in COVID-19 patients who present with persistent chest pain as MI in rapidly deteriorating cases can be missed. Prompt response includes both timely diagnosis and swift treatment.

Abstract

The coronavirus disease 2019 (COVID-19) is associated with coronary artery thrombosis. Many cases of single-vessel and few cases of two-vessel thrombosis were reported. Herein, we report a unique association in a middle-aged man diagnosed with COVID-19 and presented later with acute myocardial infarction causing cardiogenic shock. The patient was found to have three-vessel thrombosis.

Removal of senescent cells reduces the viral load and attenuates pulmonary and systemic inflammation in SARS-CoV-2-infected, aged hamsters

Older age is one of the strongest risk factors for severe COVID-19. In this study, we determined whether age-associated cellular senescence contributes to the severity of experimental COVID-19. Aged golden hamsters accumulate senescent cells in the lungs, and the senolytic drug ABT-263, a BCL-2 inhibitor, depletes these cells at baseline and during SARS-CoV-2 infection. Relative to young hamsters, aged hamsters had a greater viral load during the acute phase of infection and displayed higher levels of sequelae during the post-acute phase. Early treatment with ABT-263 lowered pulmonary viral load in aged (but not young) animals, an effect associated with lower expression of ACE2, the receptor for SARS-CoV-2. ABT-263 treatment also led to lower pulmonary and systemic levels of senescence-associated secretory phenotype factors and to amelioration of early and late lung disease. These data demonstrate the causative role of age-associated pre-existing senescent cells on COVID-19 severity and have clear clinical relevance.

Are Measles-Mumps-Rubella (MMR) Antibodies Friends or Foes for Covid-19 Disease?

Many factors have been implicated in the pathogenesis and severity of COVID-19 pandemic. A wide variation in the susceptibility for SARS-CoV-2 infection among different population, gender and age has been observed. Multiple studies investigated the relationship between the antibody's titre of previously vaccinated individuals and the susceptibility of coronavirus infection, to find a rapid effective therapy for this pandemic. This study focused on the association between measles-mumps-rubella (MMR) antibodies titre and the severity of COVID-19 infection. We aimed to investigate the correlation between the antibody's titre of MMR and the SARS-CoV-2 infection susceptibility and disease severity, in a cohort of COVID-19 Egyptian patients, compared to a control group. MMR antibody titre was measured using enzyme Linked Immune Sorbent Assay; (ELISA) for 136 COVID-19 patients and 44 healthy individuals, as control group. There were high levels of measles and mumps antibodies titer in the deteriorating cases, which could not protect from SARS-CoV-2 infection. However, the rubella antibodies might protect from SARS-CoV-2 infection, but once the infection occurs, it may aggravate the risk of case deterioration. MMR antibodies could be used as a guideline for COVID-19 symptom-severity and, in turn, may be considered as an economic prognostic marker used for early protection from multiple autoimmune organ failure.

Impact on Spine Surgery during the First Two Years of COVID-19 Pandemic: A Nationwide Study in South Korea

Since December 2019, the novel coronavirus (COVID-19) has infected people worldwide. Owing to its rapid spread, elective surgeries, including spine surgery, have been re-scheduled. We analyzed nationwide data to investigate changes in the volume of spine surgery during the first two years of the pandemic. Nationwide data from January 2016 to December 2021 were obtained. We compared the total number of patients who underwent spine surgery and related medical expenses before and during the COVID-19 pandemic. In February and September, the number of patients was significantly smaller compared to January and August, respectively. Despite the pandemic, the proportion of patients undergoing spine surgery for degenerative diseases in 2021 was the highest. In contrast, the proportions of patients undergoing spine surgery for tumors showed a continuous decrease from 2019 to 2021. Although the number of spine surgeries performed at tertiary hospitals was lowest in 2020, it was not significantly smaller than that in 2019.The number of patients who underwent spine surgery in March 2020, during the first outbreak, decreased compared to the previous month, which differed from the trend observed in the pre-COVID-19 period. However, as the pandemic continues, the impact of COVID-19 on spine surgery has become less evident.

The 21st century disaster: The COVID-19 epidemiology, risk factors and control

The 21st century will be indelible in the world as ruin of the outbreak of COVID-19 was arose in Wuhan, China has now spread all over the world, up to August 2020. This study was based on the factors affecting the epidemiology of this virus in human societies of global concern. We studied the articles published in journals on various aspects of nCoVID19. The Wikipedia and WHO situation reports have also been searched out for related information. Outcomes were followed up until 2020. The COVID-19 is a virus with pandemic potential which may continue to cause regular infection in human. The pandemic outbreak of COVID-19 threatened public health across the globe in form of system as reflected in the shape of emergency. Approximately 21 million humans are infected and 759,400 have lost their lives till 2020 in all over the world. We have described epidemiological features, reservoirs, transmission, incubation period, rate of fatality, management including recent clinical chemotherapeutic approach and preventive measurements and masses which are at risk of COVID19. This virus causes viral pneumonia when it attacks on respiratory system and multiple failure which can leads to life threatening complications. It is believed to be zoonotic importance although it is not clear from which animal and how it is transmitted. Zoonotic transmission of COVID-19 has not yet known by science. The current study will help to establish a baseline for early effective control of this rapidly spreading severe viral illness. The available data on COVID-19 indicates that older males with comorbidities would have been more infected, which can result in severe respiratory complications. Implementation of preventive measurements, investigation of proper chemotherapeutics and detection of cross species transmission agents must be ensured.

Antiviral Peptides Delivered by Chitosan-Based Nanoparticles to Neutralize SARS-CoV-2 and HCoV-OC43

The COVID-19 pandemic has made it clear that there is a crucial need for the design and development of antiviral agents that can efficiently reduce the fatality rate caused by infectious diseases. The fact that coronavirus mainly enters through the nasal epithelial cells and spreads through the nasal passage makes the nasal delivery of antiviral agents a promising strategy not only to reduce viral infection but also its transmission. Peptides are emerging as powerful candidates for antiviral treatments, showing not only a strong antiviral activity, but also improved safety, efficacy, and higher specificity against viral pathogens. Based on our previous experience on the use of chitosan-based nanoparticles to deliver peptides intra-nasally the current study aimed to explore the delivery of two-novel antiviral peptides making use of nanoparticles consisting of HA/CS and DS/CS. The antiviral peptides were chemically synthesized, and the optimal conditions for encapsulating them were selected through a combination of physical entrapment and chemical conjugation using HA/CS and DS/CS nanocomplexes. Finally, we evaluated the in vitro neutralization capacity against SARS-CoV-2 and HCoV-OC43 for potential use as prophylaxis or therapy.

In Vitro Characterization and Antiviral Susceptibility of Ophidian Serpentoviruses

Ophidian serpentoviruses, positive-sense RNA viruses in the order Nidovirales, are important infectious agents of both captive and free-ranging reptiles. Although the clinical significance of these viruses can be variable, some serpentoviruses are pathogenic and potentially fatal in captive snakes. While serpentoviral diversity and disease potential are well documented, little is known about the fundamental properties of these viruses, including their potential host ranges, kinetics of growth, environmental stability, and susceptibility to common disinfectants and viricides. To address this, three serpentoviruses were isolated in culture from three unique PCR-positive python species: Ball python (Python regius), green tree python (Morelia viridis), and Stimson's python (Antaresia stimsoni). A median tissue culture infectious dose (TCID₅₀) was established to characterize viral stability, growth, and susceptibility. All isolates showed an environmental stability of 10-12 days at room temperature (20 °C). While all three viruses produced variable peak titers on three different cell lines when incubated at 32 °C, none of the viruses detectably replicated at 35 °C. All viruses demonstrated a wide susceptibility to sanitizers, with 10% bleach, 2% chlorhexidine, and 70% ethanol inactivating the virus in one minute and 7% peroxide and a quaternary ammonium solution within three minutes. Of seven tested antiviral agents, remdesivir, ribavirin, and NITD-008, showed potent antiviral activity against the three viruses. Finally, the three isolates successfully infected 32 unique tissue culture cell lines representing different diverse reptile taxa and select mammals and birds as detected by epifluorescent immunostaining. This study represents the first characterization of in vitro properties of growth, stability, host range, and inactivation for a serpentovirus. The reported results provide the basis for procedures to mitigate the spread of serpentoviruses in captive snake colonies as well as identify potential non-pharmacologic and pharmacologic treatment options for ophidian serpentoviral infections.

Structural and non-structural proteins in SARS-CoV-2: potential aspects to COVID-19 treatment or prevention of progression of related diseases

Coronavirus disease 2019 (COVID-19) is caused by a new member of the Coronaviridae family known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). There are structural and non-structural proteins (NSPs) in the genome of this virus. S, M, H, and E proteins are structural proteins, and NSPs include accessory and replicase proteins. The structural and NSP components of SARS-CoV-2 play an important role in its infectivity, and some of them may be important in the pathogenesis of chronic diseases, including cancer, coagulation disorders, neurodegenerative disorders, and cardiovascular diseases. The SARS-CoV-2 proteins interact with targets such as angiotensin-converting enzyme 2 (ACE2) receptor. In addition, SARS-CoV-2 can stimulate pathological intracellular signaling pathways by triggering transcription factor hypoxia-inducible factor-1 (HIF-1), neuropilin-1 (NRP-1), CD147, and Eph receptors, which play important roles in the progression of neurodegenerative diseases like Alzheimer's disease, epilepsy, and multiple sclerosis, and multiple cancers such as glioblastoma, lung malignancies, and leukemias. Several compounds such as polyphenols, doxazosin, baricitinib, and ruxolitinib could inhibit these interactions. It has been demonstrated that the SARS-CoV-2 spike protein has a stronger affinity for human ACE2 than the spike protein of SARS-CoV, leading the current study to hypothesize that the newly produced variant Omicron receptor-binding domain (RBD) binds to human ACE2 more strongly than the primary strain. SARS and Middle East respiratory syndrome (MERS) viruses against structural and NSPs have become resistant to previous vaccines. Therefore, the review of recent studies and the performance of current vaccines and their effects on COVID-19 and related diseases has become a vital need to deal with the current conditions. This review examines the potential role of these SARS-CoV-2 proteins in the initiation of chronic diseases, and it is anticipated that these proteins could serve as components of an effective vaccine or treatment for COVID-19 and related diseases. Video Abstract.

QSAR and molecular docking studies on designing potent inhibitors of SARS-CoVs main protease

Background: Severe acute respiratory syndrome coronavirus (SARS-CoVs) have emerged as a global health threat, which had caused a high rate of mortality. There is an urgent need to find effective drugs against these viruses. Objective: This study aims to predict the activity of unsymmetrical aromatic disulfides by constructing a QSAR model, and to design new compounds according to the structural and physicochemical attributes responsible for higher activity towards SARS-CoVs main protease. Methods: All molecules were constructed in ChemOffice software and molecular descriptors were calculated by CODESSA software. A regression-based linear heuristic method was established by changing descriptors datasets and calculating predicted IC₅₀ values of compounds. Then, some new compounds were designed according to molecular descriptors from the heuristic method model. The compounds with predicted values smaller than a set point were constantly screened out. Finally, the properties analysis and molecular docking were conducted to further understand the structure-activity relationships of these finalized compounds. Results: The heuristic method explored the various descriptors responsible for bioactivity and gained the best linear model with R² 0.87. The success of the model fully passed the testing set validation, proving that the model has both high statistical significance and excellent predictive ability. A total of 5 compounds with ideal predicted IC₅₀ were found from the 96 newly designed derivatives and their properties analyze was carried out. Molecular docking experiments were conducted for the optimal compound 31a, which has the best compound activity with good target protein binding capability. Conclusion: The heuristic method was quite reliable for predicting IC₅₀ values of unsymmetrical aromatic disulfides. The present research provides meaningful guidance for further exploration of the highly active inhibitors for SARS-CoVs.

Determining half-life of SARS-CoV-2 antigen in respiratory secretion

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is primarily transmitted from person to person through respiratory droplets and aerosols. It is also possible for the virus to be transmitted indirectly through environmental contamination. The likelihood of environmental transmission depends on several factors, including the survival time of the virus in respiratory secretions. However, the stability of SARS-CoV-2 in respiratory secretions has not been investigated. In this study, we compared the half-life of the SARS-CoV-2 antigen in respiratory secretion under different conditions. We applied respiratory secretion (5 µL) to glass slides, air-dried the slides for 1 h, and kept them at 24 °C or 4 °C for 10 days. Respiratory secretions were also placed in test tubes (sealed to preserve moisture) and in normal saline for 10 days. The concentration of SARS-CoV-2 antigen in all samples was simultaneously measured using colloidal gold immunochromatography, and the half-life of the antigen was calculated. The half-life of the antigen in the wet (sealed tube) and saline samples at room temperature was 5.0 and 2.92 days, respectively. The half-life of the antigen in the air-dried sample at room temperature and at 4 °C was 2.93 and 11.4 days, respectively. The half-life was longer in respiratory secretions than that in normal saline. The half-life was also longer in respiratory secretions, at a lower temperature, and under wet conditions. Therefore, environmental transmission can also play a significant role in the spread of the virus. Robust prevention and control strategies could be developed based on the half-life of the antigen in respiratory secretions.

Virus diversity, wildlife-domestic animal circulation and potential zoonotic viruses of small mammals, pangolins and zoo animals

Wildlife is reservoir of emerging viruses. Here we identified 27 families of mammalian viruses from 1981 wild animals and 194 zoo animals collected from south China between 2015 and 2022, isolated and characterized the pathogenicity of eight viruses. Bats harbor high diversity of coronaviruses, picornaviruses and astroviruses, and a potentially novel genus of Bornaviridae. In addition to the reported SARSr-CoV-2 and HKU4-CoV-like viruses, picornavirus and respiroviruses also likely circulate between bats and pangolins. Pikas harbor a new clade of Embecovirus and a new genus of arenaviruses. Further, the potential cross-species transmission of RNA viruses (paramyxovirus and astrovirus) and DNA viruses (pseudorabies virus, porcine circovirus 2, porcine circovirus 3 and parvovirus) between wildlife and domestic animals was identified, complicating wildlife protection and the prevention and control of these diseases in domestic animals. This study provides a nuanced view of the frequency of host-jumping events, as well as assessments of zoonotic risk.

Minimal requirements for ISO15189 validation and accreditation of three next generation sequencing procedures for SARS-CoV-2 surveillance in clinical setting

Rapid and recurrent breakthroughs of new SARS-CoV-2 strains (variants) have prompted public health authorities worldwide to set up surveillance networks to monitor the circulation of variants of concern. The use of next-generation sequencing technologies has raised the need for quality control assessment as required in clinical laboratories. The present study is the first to propose a validation guide for SARS-CoV-2 typing using three different NGS methods fulfilling ISO15189 standards. These include the assessment of the risk, specificity, accuracy, reproducibility, and repeatability of the methods. Among the three methods used, two are amplicon-based involving reverse transcription polymerase chain reaction (Artic v3 and Midnight v1) on Oxford Nanopore Technologies while the third one is amplicon-based using reverse complement polymerase chain reaction (Nimagen) on Illumina technology. We found that all methods met the quality requirement (e.g., 100% concordant typing results for accuracy, reproducibility, and repeatability) for SARS-CoV-2 typing in clinical setting. Additionally, the typing results emerging from each of the three sequencing methods were compared using three widely known nomenclatures (WHO, Pangolineage, and Nextclade). They were also compared regarding single nucleotide variations. The outcomes showed that Artic v3 and Nimagen should be privileged for outbreak investigation as they provide higher quality results for samples that do not meet inclusion criteria for analysis in a clinical setting. This study is a first step towards validation of laboratory developed NGS tests in the context of the new European regulation for medical devices and in vitro diagnostics.

A Candidate Antigen of the Recombinant Membrane Protein Derived from the Porcine Deltacoronavirus Synthetic Gene to Detect Seropositive Pigs

Porcine deltacoronavirus (PDCoV) is an emergent swine coronavirus which infects cells from the small intestine and induces watery diarrhea, vomiting and dehydration, causing mortality in piglets (>40%). The aim of this study was to evaluate the antigenicity and immunogenicity of the recombinant membrane protein (M) of PDCoV (rM-PDCoV), which was developed from a synthetic gene obtained after an in silico analysis with a group of 138 GenBank sequences. A 3D model and phylogenetic analysis confirmed the highly conserved M protein structure. Therefore, the synthetic gene was successfully cloned in a pETSUMO vector and transformed in E. coli BL21 (DE3). The rM-PDCoV was confirmed by SDS-PAGE and Western blot with ~37.7 kDa. The rM-PDCoV immunogenicity was evaluated in immunized (BLAB/c) mice and iELISA. The data showed increased antibodies from 7 days until 28 days (p < 0.001). The rM-PDCoV antigenicity was analyzed using pig sera samples from three states located in "El Bajío" Mexico and positive sera were determined. Our results show that PDCoV has continued circulating on pig farms in Mexico since the first report in 2019; therefore, the impact of PDCoV on the swine industry could be higher than reported in other studies.

Viability of SARS-CoV-2 on lettuce, chicken, and salmon and its inactivation by peracetic acid, ethanol, and chlorine dioxide

Since the first SARS-CoV-2 outbreak in Wuhan, China, there has been continued concern over the link between SARS-CoV-2 transmission and food. However, there are few studies on the viability and removal of SARS-CoV-2 contaminating food. This study aimed to evaluate the viability of SARS-CoV-2 on food matrices, depending on storage temperature, and inactivate the virus contaminating food using disinfectants. Two SARS-CoV-2 strains (L and S types) were used to contaminate lettuce, chicken, and salmon, which were then stored at 20,4 and -40 °C. The half-life of SARS-CoV-2 at 20 °C was 3-7 h but increased to 24-46 h at 4 °C and exceeded 100 h at -40 °C. SARS-CoV-2 persisted longer on chicken or salmon than on lettuce. Treatment with 70% ethanol for 1 min inactivated 3.25 log reduction of SARS-CoV-2 inoculated on lettuce but not on chicken and salmon. ClO2 inactivated up to 2 log reduction of SARS-CoV-2 on foods. Peracetic acid was able to eliminate SARS-CoV-2 from all foods. The virucidal effect of all disinfectants used in this study did not differ between the two SARS-CoV-2 strains; therefore, they could also be effective against other SARS-CoV-2 variants. This study demonstrated that the viability of SARS-CoV-2 can be extended at 4 and -40 °C and peracetic acid can inactivate SARS-CoV-2 on food matrices.

Conception and reality: Outcome of SARS-CoV-2 infection and vaccination among Hungarian IBD patients on biologic treatments

Introduction

Inflammatory bowel disease potentially elevates the risk of infections, independently from age, while the disease activity and medical treatment(s) can also increase the risks. Nevertheless, it is necessary to clarify these preconceptions as well during the COVID-19 pandemic.

Methods

An observational, questionnaire based study was conducted in Hungary between February and August 2021. 2 questionnaires were completed. The first questionnaire surveyed the impact of the pandemic on patients with biologic treatments and assessed the severity and outcome of the infection, whereas the second one assessed vaccination rate and adverse events.

Results

472 patients participated in the study. 16.9 % of them acquired the infection and 6.3 % needed hospitalization. None of them required ICU care. Male sex elevated the risk of infection (p = 0.008), while glove (p = 0.02) and mask wearing (p = 0.005) was the most effective prevention strategy. Nevertheless, abstaining from community visits or workplace did not have an impact on the infection rate. Smoking, age, and disease type did not elevate the risk. UC patients had poorer condition during the infection (p = 0.003); furthermore, the disease activity could potentially worsen the course of infection (p = 0.072). The different biological treatments were equally safe; no difference was observed in the infection rate, course of COVID-19. Azathioprine and corticosteroids did not elevate the infection rate. 28 patients (35.0 %) suspended the ongoing biologic treatment, but it had no impact on the disease course. However, it resulted in changing the current treatment (p = 0.004). 9.8 % of the respondents were sceptic about being vaccinated, and 90 % got vaccinated. In one case, a serious flare-up occurred.

Discussion

Most patients acquired the infection at workplace. Biologic therapies had no effect on the COVID-19 infection, whereas male sex, an active disease, and UC could be larger threat than treatments. Vaccination was proved to be safe, and patient education is important to achieve mass vaccination of the population.

What do we know about the origin of COVID-19 three years later?

More than three years have passed since the first case of a new coronavirus infection (SARS-CoV-2) in the city of Wuhan (Hubei, China). The Wuhan Institute of Virology was founded in that city in 1956 and the country's first biosafety level 4 laboratory opened within that center in 2015. The coincidence that the first cases of infection emerged in the city where the virology institute's headquarters is located, the failure to 100% identify the virus' RNA in any of the coronaviruses isolated in bats, and the lack of evidence on a possible intermediate animal host in the contagion's transmission make it so that at present, there are doubts about the real origin of SARS-CoV-2. This article will review two theories: SARS-CoV-2 as a virus of zoonotic origin or as a leak from the high-level biosafety laboratory in Wuhan.

Nonsteroidal anti-inflammatory drugs (NSAIDs) and nucleotide analog GS-441524 conjugates with potent in vivo efficacy against coronaviruses

Coronaviruses (CoVs) infect a broad range of hosts, including humans and various animals, with a tendency to cross the species barrier, causing severe harm to human society and fostering the need for effective anti-coronaviral drugs. GS-441524 is a broad-spectrum antiviral nucleoside with potent anti-CoVs activities. However, its application is limited by poor oral bioavailability. Herein, we designed and synthesized several conjugates via covalently binding NSAIDs to 5'-OH of GS-441524 through ester bonds. The ibuprofen conjugate, ATV041, exhibited potent in vitro anti-coronaviral efficacy against four zoonotic coronaviruses in the alpha- and beta-genera. Oral-dosed ATV041 resulted in favorable bioavailability and rapid tissue distribution of GS-441524 and ibuprofen. In MHV-A59 infected mice, ATV041 dose-dependently decreased viral RNA replication and significantly reduced the proinflammatory cytokines in the liver and the lung at 3 dpi. As a result, the MHV-A59-induced lung and liver inflammatory injury was significantly alleviated. Taken together, this work provides a novel drug conjugate strategy to improve oral PK and offers a potent anti-coronaviral lead compound for further studies.

Intestinal Tropism of a Betacoronavirus (Merbecovirus) in Nathusius's Pipistrelle Bat (Pipistrellus nathusii), Its Natural Host

The emergence of several bat coronavirus-related disease outbreaks in human and domestic animals has fueled surveillance of coronaviruses in bats worldwide. However, little is known about how these viruses interact with their natural hosts. We demonstrate a Betacoronavirus (subgenus Merbecovirus), PN-βCoV, in the intestine of its natural host, Nathusius's Pipistrelle Bat (Pipistrellus nathusii), by combining molecular and microscopy techniques. Eighty-eight P. nathusii bat carcasses were tested for PN-βCoV RNA by RT-qPCR, of which 25 bats (28%) tested positive. PN-βCoV RNA was more often detected in samples of the intestinal tract than in other sample types. In addition, viral RNA loads were higher in intestinal samples compared to other sample types, both on average and in each individual bat. In one bat, we demonstrated Merbecovirus antigen and PN-βCoV RNA expression in intestinal epithelium and the underlying connective tissue using immunohistochemistry and in situ hybridization, respectively. These results indicate that PN-βCoV has a tropism for the intestinal epithelium of its natural host, Nathusius's Pipistrelle Bat, and imply that the fecal-oral route is a possible route of transmission. IMPORTANCE Virtually all mammal species circulate coronaviruses. Most of these viruses will infect one host species; however, coronaviruses are known to include species that can infect multiple hosts, for example the well-known virus that caused a pandemic, SARS-CoV-2. Chiroptera (bats) include over 1,400 different species, which are expected to harbor a great variety of coronaviruses. However, we know very little about how any of these coronaviruses interact with their bat hosts; for example, we do not know their modes of transmissions, or which cells they infect. Thus, we have a limited understanding of coronavirus infections in this important host group. The significance of our study is that we learned that a bat coronavirus that occurs in a common bat species in Europe has a tropism for the intestines. This implies the fecal-oral route is a likely transmission route.

Aerogels based on cationically modified chitosan and poly(vinyl alcohol) for efficient capturing of viruses

In this study, we developed a new filtering bioaerogel based on linear polyvinyl alcohol (PVA) and the cationic derivative of chitosan (N-[(2-hydroxy-3-trimethylamine) propyl] chitosan chloride, HTCC) with a potential antiviral application. A strong intermolecular network architecture was formed thanks to the introduction of linear PVA chains, which can efficiently interpenetrate the glutaraldehyde(GA)-crosslinked HTCC chains. The morphology of the obtained structures was examined using scanning electron microscopy (SEM) and atomic force microscopy (AFM). The aerogels and modified polymers' elemental composition (including the chemical environment) was determined using X-ray photoelectron spectroscopy (XPS). New aerogels with more than twice as much developed micro- and mesopore space and BET-specific surface area were obtained concerning the starting sample chitosan aerogel crosslinked by glutaraldehyde (Chit/GA). The results obtained from the XPS analysis showed the presence of cationic 3-trimethylammonium groups on the surface of the aerogel, which can interact with viral capsid proteins. No cytotoxic effect of HTCC/GA/PVA aerogel was also observed on fibroblast cells of the NIH3T3 line. Furthermore, the HTCC/GA/PVA aerogel has been shown that efficiently traps mouse hepatitis virus (MHV) from suspension. The presented concept of aerogel filters for virus capture based on modified chitosan and polyvinyl alcohol has a high application potential.

Effect of zinc supplementation on symptom reduction and length of hospital stay among pediatric patients with Coronavirus Disease 2019 (COVID-19)

Objectives

Zinc is considered an essential multipurpose trace element because of its ability to act as a cofactor and signaling molecule. As reported in earlier studies of pediatric respiratory infection management, zinc exhibits potent immunoregulatory and antiviral properties, but its effects on pediatric patients with COVID-19 remain unknown. The aim of this study was to determine the extent to which zinc supplementation improves COVID-19 symptoms, length of hospitalization and, to determine how zinc supplementation impacts ICU admission, in-hospital mortality, need for ventilation, duration of ventilation, need for vasopressors, development of liver injury, or respiratory failure.

Methods

Pediatric patients younger than 18 years with confirmed COVID-19 infection during the study period (March 1, 2020, to December 31, 2021) were recruited for this retrospective cohort study. The study population was divided into two arms (zinc/no zinc supplementation as an adjunct to standard therapy).

Results

Of 169 hospitalized patients who were screened, 101 met the inclusion criteria. No statistically significant association was found between the administration of zinc as adjunctive therapy and symptom reduction, intensive care unit (ICU) admission, or mortality (p = 0.105; p = 0.941, and p = 0.073, respectively). However, zinc supplementation was associated with a statistically significant reduction in respiratory failure and length of hospitalization (p = 0.004 and p = 0.017, respectively), also, zinc administration was associated with elevated serum creatinine (p = 0.01*).

Conclusions

Among pediatric patients with COVID-19, zinc supplementation was associated with shorter hospital stay. However, there was no significant difference between the two groups in terms of symptom improvement, in-hospital mortality, or ICU admission. In addition, the study raises question about the possibility of kidney injury as indicated by high levels of serum creatinine.

Ammi-visnaga extract; a novel phyto-antiviral agent against bovine rotavirus

The spread of bovine rotavirus has a great impact on animal productivity, milk products, and human public health. Thus, this study aimed to develop a novel, effective and accessible Phyto-antiviral treatment made from methanolic Ammi-visnaga seed extract against rotavirus infection. Rotaviruses were isolated from raw milk and cottage cheese samples randomly collected from Cairo and Qalubia governorates. They were all identified serologically, however, only three of them were both biologically and molecularly confirmed. The methanolic extract derived from Khella seeds (MKSE) was chemically analyzed with mass chromatography. The cellular toxicity of MKSE was tested on Caco-2 cells and its antiviral activity against one of the isolated bovine rotaviruses (BRVM1) was tested by both the cytopathic inhibition assay and the plaque reduction assay. Our results showed that 17.3% of the total collected 150 dairy samples were bovine rotavirus antigen positive. Three representatives of them were phylogenetically identified to be included in group A based on a 379 bp coat protein gene. Visnagin, Benzopyran, Khellin, and Benzenepropanoic acid were the major active components found in the MKSE. The maximum non-toxic concentration of MKSE was 5 µg/mL and the CC50 value was 417 µg/mL. The MKSE exhibited in-vitro antiviral activity against BRVM1 indicated by inhibition of the viral cytopathic effect (SI = 204.5, IP = 98%), causing a 1.5 log decrease in BVRM1 TCID50 and reducing the viral plaques count by the percentage of 93.14% at MNTC (5 ug/ml). In conclusion, our study showed that bovine rotavirus represents a severe health problem that needs attention in Egypt, and it supports using MKSE as a potential natural anti-rotavirus agent.

Molecular docking, molecular dynamics simulation and MM-GBSA studies of the activity of glycyrrhizin relevant substructures on SARS-CoV-2 RNA-dependent-RNA polymerase

SARS-CoV-2 is the causative agent of Coronavirus Disease (COVID-19), which is a life-threatening disease. The World Health Organization has classified COVID-19 as a severe worldwide public health pandemic due to its high death rate, quick transmission, and lack of medicines. To counteract the recurrence of the severe acute respiratory syndrome, active antiviral medications are urgently required. Glycyrrhizin was documented with activity on different viral proteins, including SARS-CoV-2; in this study, the activity of glycyrrhizin and its substructures (604 molecules) were screened on SARS-CoV-2 RNA-dependent-RNA polymerase using molecular docking, molecular dynamic (MD) simulation, and MM/GBSA. Sixteen molecules exhibited docking energy higher than -7 kcal/mol; four compounds (10772603, 101088272, 154730753 and glycyrrhizin) showed the highest binding energy, and good stability during MD simulation. The glycyrrhizin compound exhibited favorable docking energy (-7.9 kcal/mol), and it was the most stable complex during MD simulation. The predicted binding free energy of the glycyrrhizin complex was -57 ± 8 kcal/mol. These findings suggest that this molecule, after more validation, could become a good candidate for developing and manufacturing an anti-SARS-CoV-2 medication.Communicated by Ramaswamy H. Sarma.

Cellular senescence as a source of SARS-CoV-2 quasispecies

In-depth analysis of SARS-CoV-2 biology and pathogenesis is rapidly unraveling the mechanisms through which the virus induces all aspects of COVID-19 pathology. Emergence of hundreds of variants and several important variants of concern has focused research on the mechanistic elucidation of virus mutagenesis. RNA viruses evolve quickly either through the error-prone polymerase or the RNA-editing machinery of the cell. In this review, we are discussing the links between cellular senescence, a natural aging process that has been recently linked to SARS-CoV-2 infection, and virus mutagenesis through the RNA-editing enzymes APOBEC. The action of APOBEC, enhanced by cellular senescence, is hypothesized to assist the emergence of novel variants, called quasispecies, within a cell or organism. These variants when introduced to the community may lead to the generation of a variant of concern, depending on fitness and transmissibility of the new genome. Such a mechanism of virus evolution may highlight the importance of inhibitors of cellular senescence during SARS-CoV-2 clinical treatment.

The Role of Immunity in the Pathogenesis of SARS-CoV-2 Infection and in the Protection Generated by COVID-19 Vaccines in Different Age Groups

This study aims to review the available data regarding the central role of immunity in combating SARS-CoV-2 infection and in the generation of protection by vaccination against COVID-19 in different age groups. Physiologically, the immune response and the components involved in it are variable, both functionally and quantitatively, in neonates, infants, children, adolescents, and adults. These immunological differences are mirrored during COVID-19 infection and in the post-vaccination period. The outcome of SARS-CoV-2 infection is greatly dependent on the reaction orchestrated by the immune system. This is clearly obvious in relation to the clinical status of COVID-19 infection, which can be symptomless, mild, moderate, or severe. Even the complications of the disease show a proportional pattern in relation to the immune response. On the contrary, the commonly used anti-COVID-19 vaccines generate protective humoral and cellular immunity. The magnitude of this immunity and the components involved in it are discussed in detail. Furthermore, many of the adverse effects of these vaccines can be explained on the basis of immune reactions against the different components of the vaccines. Regarding the appropriate choice of vaccine for different age groups, many factors have to be considered. This is a cornerstone, particularly in the following age groups: 1 day to 5 years, 6 to 11 years, and 12 to 17 years. Many factors are involved in deciding the route, doses, and schedule of vaccination for children. Another important issue in this dilemma is the hesitancy of families in making the decision about whether to vaccinate their children. Added to these difficulties is the choice by health authorities and governments concerning whether to make children's vaccination compulsory. In this respect, although rare and limited, adverse effects of vaccines in children have been detected, some of which, unfortunately, have been serious or even fatal. However, to achieve comprehensive control over COVID-19 in communities, both children and adults have to be vaccinated, as the former group represents a reservoir for viral transmission. The understanding of the various immunological mechanisms involved in SARS-CoV-2 infection and in the preparation and application of its vaccines has given the sciences a great opportunity to further deepen and expand immunological knowledge. This will hopefully be reflected positively on other diseases through gaining an immunological background that may aid in diagnosis and therapy. Humanity is still in continuous conflict with SARS-CoV-2 infection and will be for a while, but the future is expected to be in favor of the prevention and control of this disease.

Deep Learning-Based Bioactive Therapeutic Peptide Generation and Screening

Many bioactive peptides demonstrated therapeutic effects over complicated diseases, such as antiviral, antibacterial, anticancer, etc. It is possible to generate a large number of potentially bioactive peptides using deep learning in a manner analogous to the generation of de novo chemical compounds using the acquired bioactive peptides as a training set. Such generative techniques would be significant for drug development since peptides are much easier and cheaper to synthesize than compounds. Despite the limited availability of deep learning-based peptide-generating models, we have built an LSTM model (called LSTM_Pep) to generate de novo peptides and fine-tuned the model to generate de novo peptides with specific prospective therapeutic benefits. Remarkably, the Antimicrobial Peptide Database has been effectively utilized to generate various kinds of potential active de novo peptides. We proposed a pipeline for screening those generated peptides for a given target and used the main protease of SARS-COV-2 as a proof-of-concept. Moreover, we have developed a deep learning-based protein-peptide prediction model (DeepPep) for rapid screening of the generated peptides for the given targets. Together with the generating model, we have demonstrated that iteratively fine-tuning training, generating, and screening peptides for higher-predicted binding affinity peptides can be achieved. Our work sheds light on developing deep learning-based methods and pipelines to effectively generate and obtain bioactive peptides with a specific therapeutic effect and showcases how artificial intelligence can help discover de novo bioactive peptides that can bind to a particular target.

HuCoPIA: An Atlas of Human vs. SARS-CoV-2 Interactome and the Comparative Analysis with Other Coronaviridae Family Viruses

SARS-CoV-2, a novel betacoronavirus strain, has caused a pandemic that has claimed the lives of nearly 6.7M people worldwide. Vaccines and medicines are being developed around the world to reduce the disease spread, fatality rates, and control the new variants. Understanding the protein-protein interaction mechanism of SARS-CoV-2 in humans, and their comparison with the previous SARS-CoV and MERS strains, is crucial for these efforts. These interactions might be used to assess vaccination effectiveness, diagnose exposure, and produce effective biotherapeutics. Here, we present the HuCoPIA database, which contains approximately 100,000 protein-protein interactions between humans and three strains (SARS-CoV-2, SARS-CoV, and MERS) of betacoronavirus. The interactions in the database are divided into common interactions between all three strains and those unique to each strain. It also contains relevant functional annotation information of human proteins. The HuCoPIA database contains SARS-CoV-2 (41,173), SARS-CoV (31,997), and MERS (26,862) interactions, with functional annotation of human proteins like subcellular localization, tissue-expression, KEGG pathways, and Gene ontology information. We believe HuCoPIA will serve as an invaluable resource to diverse experimental biologists, and will help to advance the research in better understanding the mechanism of betacoronaviruses.

Unveiling the Potentiality of Shikonin Derivatives Inhibiting SARS-CoV-2 Main Protease by Molecular Dynamic Simulation Studies

Shikonin, a phytochemical present in the roots of Lithospermum erythrorhizon, is well-known for its broad-spectrum activity against cancer, oxidative stress, inflammation, viruses, and anti-COVID-19 agents. A recent report based on a crystallographic study revealed a distinct conformation of shikonin binding to the SARS-CoV-2 main protease (M^pro), suggesting the possibility of designing potential inhibitors based on shikonin derivatives. The present study aimed to identify potential shikonin derivatives targeting the M^pro of COVID-19 by using molecular docking and molecular dynamics simulations. A total of 20 shikonin derivatives were screened, of which few derivatives showed higher binding affinity than shikonin. Following the MM-GBSA binding energy calculations using the docked structures, four derivatives were retained with the highest binding energy and subjected to molecular dynamics simulation. Molecular dynamics simulation studies suggested that alpha-methyl-n-butyl shikonin, beta-hydroxyisovaleryl shikonin, and lithospermidin-B interacted with two conserved residues, His41 and Cys145, through multiple bonding in the catalytic sites. This suggests that these residues may effectively suppress SARS-CoV-2 progression by inhibiting M^pro. Taken together, the present in silico study concluded that shikonin derivatives may play an influential role in M^pro inhibition.

Current and Emerging Knowledge in COVID-19

COVID-19 has emerged as a pandemic leading to a global public health crisis of unprecedented morbidity. A comprehensive insight into the imaging of COVID-19 has enabled early diagnosis, stratification of disease severity, and identification of potential sequelae. The evolution of COVID-19 can be divided into early infectious, pulmonary, and hyperinflammatory phases. Clinical features, imaging features, and management are different among the three phases. In the early stage, peripheral ground-glass opacities are predominant CT findings, and therapy directly targeting SARS-CoV-2 is effective. In the later stage, organizing pneumonia or diffuse alveolar damage pattern are predominant CT findings and anti-inflammatory therapies are more beneficial. The risk of severe disease or hospitalization is lower in breakthrough or Omicron variant infection compared with nonimmunized or Delta variant infections. The protection rates of the fourth dose of mRNA vaccination were 34% and 67% against overall infection and hospitalizations for severe illness, respectively. After acute COVID-19 pneumonia, most residual CT abnormalities gradually decreased in extent, but they may remain as linear or multifocal reticular or cystic lesions. Advanced insights into the pathophysiologic and imaging features of COVID-19 along with vaccine benefits have improved patient care, but emerging knowledge of post-COVID-19 condition, or long COVID, also presents radiology with new challenges.

Coronaviruses: Troubling Crown of the Animal Kingdom

The existence of coronaviruses has been known for many years. These viruses cause significant disease that primarily seems to affect agricultural species. Human coronavirus disease due to the 2002 outbreak of Severe Acute Respiratory Syndrome and the 2012 outbreak of Middle East Respiratory Syndrome made headlines; however, these outbreaks were controlled, and public concern quickly faded. This complacency ended in late 2019 when alarms were raised about a mysterious virus responsible for numerous illnesses and deaths in China. As we now know, this novel disease called Coronavirus Disease 2019 (COVID-19) was caused by Severe acute respiratory syndrome-related-coronavirus-2 (SARS-CoV-2) and rapidly became a worldwide pandemic. Luckily, decades of research into animal coronaviruses hastened our understanding of the genetics, structure, transmission, and pathogenesis of these viruses. Coronaviruses infect a wide range of wild and domestic animals, with significant economic impact in several agricultural species. Their large genome, low dependency on host cellular proteins, and frequent recombination allow coronaviruses to successfully cross species barriers and adapt to different hosts including humans. The study of the animal diseases provides an understanding of the virus biology and pathogenesis and has assisted in the rapid development of the SARS-CoV-2 vaccines. Here, we briefly review the classification, origin, etiology, transmission mechanisms, pathogenesis, clinical signs, diagnosis, treatment, and prevention strategies, including available vaccines, for coronaviruses that affect domestic, farm, laboratory, and wild animal species. We also briefly describe the coronaviruses that affect humans. Expanding our knowledge of this complex group of viruses will better prepare us to design strategies to prevent and/or minimize the impact of future coronavirus outbreaks.

The COVID-19 pandemic in sub-Saharan Africa: The significance of presumed immune sufficiency

A novel coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in China in 2019 and later ignited a global pandemic. Contrary to expectations, the effect of the pandemic was not as devastating to Africa and its young population compared to the rest of the world. To provide insight into the possible reasons for the presumed immune sufficiency to coronavirus disease 2019 (COVID-19) in Africa, this review critically examines literature published from 2020 onwards on the dynamics of COVID-19 infection and immunity and how other prevalent infectious diseases in Africa might have influenced the outcome of COVID-19. Studies characterising the immune response in patients with COVID-19 show that the correlates of protection in infected individuals are T-cell responses against the SARS-CoV-2 spike protein and neutralising titres of immunoglobin G and immunoglobin A antibodies. In some other studies, substantial pre-existing T-cell reactivity to SARS-CoV-2 was detected in many people from diverse geographical locations without a history of exposure. Certain studies also suggest that innate immune memory, which offers protection against reinfection with the same or another pathogen, might influence the severity of COVID-19. In addition, an initial analysis of epidemiological data showed that COVID‑19 cases were not severe in some countries that implemented universal Bacillus Calmette-Guerin (BCG) vaccination policies, thus supporting the potential of BCG vaccination to boost innate immunity. The high burden of infectious diseases and the extensive vaccination campaigns previously conducted in Africa could have induced specific and non-specific protective immunity to infectious pathogens in Africans.

Transmissible Gastroenteritis Virus: An Update Review and Perspective

Transmissible gastroenteritis virus (TGEV) is a member of the alphacoronavirus genus, which has caused huge threats and losses to pig husbandry with a 100% mortality in infected piglets. TGEV is observed to be recombining and evolving unstoppably in recent years, with some of these recombinant strains spreading across species, which makes the detection and prevention of TGEV more complex. This paper reviews and discusses the basic biological properties of TGEV, factors affecting virulence, viral receptors, and the latest research advances in TGEV infection-induced apoptosis and autophagy to improve understanding of the current status of TGEV and related research processes. We also highlight a possible risk of TGEV being zoonotic, which could be evidenced by the detection of CCoV-HuPn-2018 in humans.