SARS-CoV-2: an Emerging Coronavirus that Causes a Global Threat

SARS-CoV-2 Non-Structural Proteins and Their Roles in Host Immune Evasion

Coronavirus disease 2019 (COVID-19) has caused an unprecedented global crisis and continues to threaten public health. The etiological agent of this devastating pandemic outbreak is the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). COVID-19 is characterized by delayed immune responses, followed by exaggerated inflammatory responses. It is well-established that the interferon (IFN) and JAK/STAT signaling pathways constitute the first line of defense against viral and bacterial infections. To achieve viral replication, numerous viruses are able to antagonize or hijack these signaling pathways to attain productive infection, including SARS-CoV-2. Multiple studies document the roles of several non-structural proteins (NSPs) of SARS-CoV-2 that facilitate the establishment of viral replication in host cells via immune escape. In this review, we summarize and highlight the functions and characteristics of SARS-CoV-2 NSPs that confer host immune evasion. The molecular mechanisms mediating immune evasion and the related potential therapeutic strategies for controlling the COVID-19 pandemic are also discussed.

Epitope mapping of severe acute respiratory syndrome coronavirus 2 neutralizing receptor binding domain-specific monoclonal antibodies

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the outbreak led to the coronavirus disease 2019 (COVID-19) pandemic. Receptor binding domain (RBD) of spike (S) protein of SARS-CoV-2 is considered as a major target for immunotherapy and vaccine design. Here, we generated and characterized a panel of anti-RBD monoclonal antibodies (MAbs) isolated from eukaryotic recombinant RBD-immunized mice by hybridoma technology. Epitope mapping was performed using a panel of 20-mer overlapping peptides spanning the entire sequence of the RBD protein from wild-type (WT) Wuhan strain by enzyme-linked immunosorbent assay (ELISA). Several hybridomas showed reactivity toward restricted RBD peptide pools by Pepscan analysis, with more focus on peptides encompassing aa 76-110 and 136-155. However, our MAbs with potent neutralizing activity which block SARS-CoV-2 spike pseudovirus as well as the WT virus entry into angiotensin-converting enzyme-2 (ACE2) expressing HEK293T cells showed no reactivity against these peptides. These findings, largely supported by the Western blotting results suggest that the neutralizing MAbs recognize mainly conformational epitopes. Moreover, our neutralizing MAbs recognized the variants of concern (VOC) currently in circulation, including alpha, beta, gamma, and delta by ELISA, and neutralized alpha and omicron variants at different levels by conventional virus neutralization test (CVNT). While the neutralization of MAbs to the alpha variant showed no substantial difference as compared with the WT virus, their neutralizing activity was lower on omicron variant, suggesting the refractory effect of mutations in emerging variants against this group of neutralizing MAbs. Also, the binding reactivity of our MAbs to delta variant showed a modest decline by ELISA, implying that our MAbs are insensitive to the substitutions in the RBD of delta variant. Our data provide important information for understanding the immunogenicity of RBD, and the potential application of the novel neutralizing MAbs for passive immunotherapy of SARS-CoV-2 infection.

Liposome encapsulated clodronate mediated elimination of pathogenic macrophages and microglia: A promising pharmacological regime to defuse cytokine storm in COVID-19

The emergence of new SARS-CoV-2 variants continues to pose an enormous public health concern. The SARS-CoV-2 infection disrupted host immune response accounting for cytokine storm has been linked to multiorgan failure and mortality in a significant portion of positive cases. Abruptly activated macrophages have been identified as the key pathogenic determinant of cytokine storm in COVID-19. Besides, reactive microglia have been known to discharge a surplus amount of proinflammatory factors leading to neuropathogenic events in the brains of SARS-CoV-2 infected individuals. Considering the fact, depletion of activated macrophages and microglia could be proposed to eradicate the life-threatening cytokine storm in COVID-19. Clodronate, a non-nitrogenous bisphosphonate drug has been identified as a potent macrophage and microglial depleting agent. While recent advancement in the field of liposome encapsulation technology offers the most promising biological tool for drug delivery, liposome encapsulated clodronate has been reported to effectively target and induce prominent phagocytic cell death in activated macrophages and microglia compared to free clodronate molecules. Thus, in this review article, we emphasize that depletion of activated macrophages and microglial cells by administration of liposome encapsulated clodronate can be a potential therapeutic strategy to diminish the pathogenic cytokine storm and alleviate multiorgan failure in COVID-19. Moreover, recently developed COVID-19 vaccines appear to render the chronic activation of macrophages accounting for immunological dysregulation in some cases. Therefore, the use of liposome encapsulated clodronate can also be extended to the clinical management of unforeseen immunogenic reactions resulting from activated macrophages associated adverse effects of COVID-19 vaccines.

Laboratory and Point-of-Care Testing for COVID-19: A Review of Recent Developments

With the emergence of Coronavirus infection called COVID-19, testing is essential for containment and mitigation purposes. In a pandemic, control is essential to limit the spread of any virus. Initially, contact tracing was not available which ultimately led to the 2020 pandemic. However, with the development of COVID-19 rapid testing, the rate of infections has lessened and has allowed for some return to normalcy. In this review, we discuss the various antibody, antigens, and molecular tests that have been given emergency authorization (EA) from the Food and Drug Administration (FDA). Moreover, we will discuss the various point-of-care tests as well as the specificity and sensitivity that are associated with each testing kit. With appropriate testing, we can be aware of how the virus spreads and how prevalent it remains.

State-of-the-Art Smart and Intelligent Nanobiosensors for SARS-CoV-2 Diagnosis

The novel coronavirus appeared to be a milder infection initially, but the unexpected outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), commonly called COVID-19, was transmitted all over the world in late 2019 and caused a pandemic. Human health has been disastrously affected by SARS-CoV-2, which is still evolving and causing more serious concerns, leading to the innumerable loss of lives. Thus, this review provides an outline of SARS-CoV-2, of the traditional tools to diagnose SARS-CoV-2, and of the role of emerging nanomaterials with unique properties for fabricating biosensor devices to diagnose SARS-CoV-2. Smart and intelligent nanomaterial-enabled biosensors (nanobiosensors) have already proven their utility for the diagnosis of several viral infections, as various detection strategies based on nanobiosensor devices are already present, and several other methods are also being investigated by researchers for the determination of SARS-CoV-2 disease; however, considerably more is undetermined and yet to be explored. Hence, this review highlights the utility of various nanobiosensor devices for SARS-CoV-2 determination. Further, it also emphasizes the future outlook of nanobiosensing technologies for SARS-CoV-2 diagnosis.

Lessons from SARS-CoV, MERS-CoV, and SARS-CoV-2 Infections: What We Know So Far

Within past decades, human infections with emerging and reemerging zoonotic viral pathogens have raised the eminent public health concern. Since November 2002, three highly pathogenic and major deadly human coronaviruses of the βετα-genera (β-hCoVs), namely, severe acute respiratory distress syndrome-coronavirus (SARS-CoV), middle east respiratory syndrome-coronavirus (MERS-CoV), and SARS-CoV-2, have been globally emerged and culminated in the occurrence of SARS epidemic, MERS outbreak, and coronavirus disease 19 (COVID-19) pandemic, respectively. The global emergence and spread of these three major deadly β-hCoVs have extremely dreadful impacts on human health and become an economic burden. Unfortunately, clear specific and highly efficient medical countermeasures for these three β-hCoVs and their underlying fatal illnesses remain under development. Although they belong to the same family and share many features and convergent evolution, these three deadly β-hCoVs have some important and obvious differences. By utilizing their lessons and gaining a deeper understanding of these β-hCoVs, we can identify areas of improvement and provide preparedness plans for fighting and controlling the future reemerging human infections that might arise from them or from other potential pathogenic hCoVs. Therefore, this review summarizes the state-of-the-art information and compares the similarities and dissimilarities between SARS-CoV, MERS-CoV, and SARS-CoV-2, in terms of their evolution trait, genome organization, host cell entry mechanisms, tissue infectivity tropisms, transmission routes and contagiousness, and the clinical characteristics, laboratory features, and immunological abnormalities of their related illnesses. It also provides an overview of the emerging SARS-CoV-2 variants. Additionally, it discusses the challenges of the most proposed treatment options for SARS-CoV-2 infections.

The role of remote sensing during a global disaster: COVID-19 pandemic as case study

Remotely sensed imagery is used as a tool to aid decision makers and scientists in a variety of fields. A recent world event in which satellite imagery was extensively relied on by a variety of stakeholders was the COVID-19 pandemic. In this article we aim to give an overview of the types of information offered through remote sensing (RS) to help address different issues related to the pandemic. We also discuss about the stakeholders that benefited from the data, and the value added by its availability. The content is presented under four sub-sections; namely (1) the use of RS in real-time decision-making and strategic planning during the pandemic; how RS revealed the (2) environmental changes and (3) social and economic impacts caused by the pandemic. And (4) how RS informed our understanding of the epidemiology of SARS-CoV-2, the pathogen responsible for the pandemic. High resolution optical imagery offered updated on-the-ground data for e.g., humanitarian aid organizations, and informed operational decision making of shipping companies. Change in the intensity of air and water pollution after reduced anthropogenic activities around the world were captured by remote sensing - supplying concrete evidence that can help inform improved environmental policy. Several economic indicators were measured from satellite imagery, showing the spatiotemporal component of economic impacts caused by the global pandemic. Finally, satellite based meteorological data supported epidemiological studies of environmental disease determinants. The varied use of remote sensing during the COVID-19 pandemic affirms the value of this technology to society, especially in times of large-scale disasters.

Evaluation of apigenin-based biflavonoid derivatives as potential therapeutic agents against viral protease (3CLpro) of SARS-CoV-2 via molecular docking, molecular dynamics and quantum mechanics studies

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of the pandemic COVID-19 disease that affects human respiratory function. Despite the scientific progression made in the development of the vaccine, there is an urgent need for the discovery of antiviral drugs for better performance at different stages of SARS-CoV-2 reproduction. The main protease (Mpro or 3CLpro) plays a pivotal role in the life cycle of the virus, making it an attractive target for the development of antiviral agents effective against the new strains of coronaviruses (CoVs). In this study, a series of apigenin-based natural biflavonoid derivatives as potential inhibitors of coronaviruses 3CLpro was investigated by in silico approaches. For this purpose, the molecular docking was performed to analyze the interaction of the natural biflavonoids with SARS-Cov-2 main protease and for further investigation, docking to the 3CLpro of SARS-CoV and MERS-CoV. Based on docking scores and comparison with the reference inhibitors (ritonavir and lopinavir), more than half of the biflavonoids had strong interactions with the residues of the binding pocket of the coronaviruses 3CLpro and exhibited better binding affinities toward the main protease than ritonavir and lopinavir. The top biflavonoids were further explored through molecular dynamics simulation, binding free energy calculation and residual energy contributions estimated by the MM-PBSA. Also, drug likeness property investigation by Swiss ADME tools and density functional theory (DFT) calculations were performed. The results confirmed that the 3CLpro-amentoflavone, 3CLpro-bilobetin, 3CLpro-ginkgetin, and 3CLpro-sotetsuflavone complexes possess a large amount of dynamic properties such as high stability, significant binding energy and fewer conformation fluctuations. Also, the pharmacokinetics and drug-likeness studies and HOMO-LUMO and DFT descriptor values indicated a promising result of the selected natural biflavonoids. Overall findings indicate that the apigenin-based biflavonoids may inhibit COVID-19 by significant interactions in the binding pocket and those results can pave the way in drug discovery although the effectiveness of these bioactive compounds should be further validated by in-vitro and in-vivo investigations. Communicated by Ramaswamy H. Sarma.

An Assessment of the Profile and Predictors of Outcomes in COVID-19 Patients Hospitalized in a Tertiary Care Institute in Central India

Background

Coronavirus disease 2019 (COVID-19) is the largest pandemic that has affected people around the globe. Various researches have been conducted worldwide, but there is a scarcity of data from Central India on the relationship between several risk factors for infection and mortality. Our study assessed the predictors and patient profiles of those with COVID-19, which will aid in prioritizing patient treatment and preventive measures.

Methods

A retrospective study was done between March and December 2020. The study included 5,552 COVID-19 patients admitted to the All India Institute of Medical Sciences (AIIMS), Raipur. A validated questionnaire form provided by the WHO was used. Data for multiple clinical and nonclinical parameters were collected, and analysis was done using SPSS version 26 (IBM Corp., Armonk, NY, USA) and STATA version 12 (StataCorp LLC, College Station, TX, USA). Mortality and risk assessment of patients was done using multivariate logistic regression.

Result

In our study cohort of 5,552 COVID-19 patients, the median age was found to be 47 years (interquartile range (IQR): 31-60 years; range: 14-100 years), and 3,557 (64%) were male. Predominantly, patients presented with fever (41.30%), cough (40.20%), and dyspnea (29.29%). The major comorbidities were hypertension (29.70%), diabetes (25.40%), and chronic cardiac disease (5.79%). The common complications were liver dysfunction (26.83%), viral pneumonitis (23.66%), acute renal injury (15.25%), and acute respiratory distress syndrome (ARDS) (13.41%). In multivariate analysis, age (more than 40 years) (odds ratio (OR): 2.63; 95% confidence interval (CI): 1.531-4.512; p<0.001), diabetes (OR: 1.61; 95% CI: 1.088-2.399; p=0.017), obesity (OR: 6.88; 95% CI: 2.188-12.153; p=0.004), leukocytosis (OR: 1.74; 95% CI: 1.422-2.422; p<0.001), lymphocytopenia (OR: 2.54, 95% CI: 1.718-3.826; p<0.001), thrombocytopenia (OR: 1.15; 95% CI: 1.777-8.700; p=0.001), and ferritin concentration > 1,000 ng/mL (OR: 4.67; 95% CI: 1.991-10.975; p<0.001) were the independent predictors of mortality among COVID-19 patients.

Conclusion

The leading comorbidities in our study were hypertension, followed by diabetes. Patients who were 40 years or older, obese patients, and diabetic patients have a higher mortality risk. The poor prognostic predictors in COVID-19 patients were high ferritin levels (>1,000 ng/mL), leukocytosis, lymphocytopenia, and thrombocytopenia.

Synthesis and Biological Evaluation of Imadazo[1,2-a]pyrazines as Anticancer and Antiviral Agents through Inhibition of CDK9 and Human Coronavirus

In this work, novel imadazo[1,2-a]pyrazine derivatives were synthesized and evaluated as CDK9 inhibitors. The results of CDK9 assay showed that the derivatives with pyridin-4-yl in position 2 and benzyl in position 3 of imadazo[1,2-a]pyrazine 3c displayed the most potent CDK9 inhibitory activity with IC₅₀ of 0.16 µM. The anti-proliferative effect of the new compounds was examined against breast cancer (MCF7), colorectal cancer (HCT116), and chronic myelogenous leukaemia (K652) cell lines. The data of MTT assay showed that the cytotoxic effect of the inhibitors is correlated to their inhibitory activity against CDK9. Compound 3c exhibited the most potent cytotoxicity effect with average IC₅₀s of three cell lines of 6.66 µM. The drug likeness properties of 3c were predicated in silico and demonstrated that 3c have reasonable physiochemical and pharmacokinetic properties. Selected derivatives were assessed in antiviral assay against human coronavirus 229E. The results of this assay showed that the derivative with pyridin-4-yl in position 2 and cyclohexyl in position 3 of imadazo[1,2-a]pyrazine 3b exhibited the most potent anti-coronaviral activity with IC₅₀ of 56.96 µM and selectivity index of 7.14. The target predication result revealed that 3b showed high affinity to protease enzyme. Docking studies of 3b with COVID-19 main protease was conducted and showed good binding affinity, which confirmed the in vitro assay data.

SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development

The pandemic caused by the SARS-CoV-2 virus, the agent responsible for the COVID-19 disease, has affected millions of people worldwide. There is constant search for new therapies to either prevent or mitigate the disease. Fortunately, we have observed the successful development of multiple vaccines. Most of them are focused on one viral envelope protein, the spike protein. However, such focused approaches may contribute for the rise of new variants, fueled by the constant selection pressure on envelope proteins, and the widespread dispersion of coronaviruses in nature. Therefore, it is important to examine other proteins, preferentially those that are less susceptible to selection pressure, such as the nucleocapsid (N) protein. Even though the N protein is less accessible to humoral response, peptides from its conserved regions can be presented by class I Human Leukocyte Antigen (HLA) molecules, eliciting an immune response mediated by T-cells. Given the increased number of protein sequences deposited in biological databases daily and the N protein conservation among viral strains, computational methods can be leveraged to discover potential new targets for SARS-CoV-2 and SARS-CoV-related viruses. Here we developed SARS-Arena, a user-friendly computational pipeline that can be used by practitioners of different levels of expertise for novel vaccine development. SARS-Arena combines sequence-based methods and structure-based analyses to (i) perform multiple sequence alignment (MSA) of SARS-CoV-related N protein sequences, (ii) recover candidate peptides of different lengths from conserved protein regions, and (iii) model the 3D structure of the conserved peptides in the context of different HLAs. We present two main Jupyter Notebook workflows that can help in the identification of new T-cell targets against SARS-CoV viruses. In fact, in a cross-reactive case study, our workflows identified a conserved N protein peptide (SPRWYFYYL) recognized by CD8⁺ T-cells in the context of HLA-B7⁺. SARS-Arena is available at https://github.com/KavrakiLab/SARS-Arena.

Effect of natural products use prior to infection with COVID-19 on disease severity and hospitalization: A self-reported cross-sectional survey study

Background: Managing coronavirus disease 2019 (COVID-19) using available resources is essential to reduce the health burden of disease. The severity of COVID-19 is affected by nutritional status. In this study the effect of natural product use prior to infection with COVID-19 on disease severity and hospitalization was explored.

Methods: This was a cross-sectional study. Between March and July 2021, a self-administered survey was conducted in Jordan. Individuals who recovered from COVID-19 and were ≥18 years old were the study population. Study measures included the use of natural products, COVID-19 severity, and hospitalization status. A multivariate regression model was used for statistical analysis.

Results: The mean age (mean ± SD) of the study sample (n=2,148) was 40.25 ± 15.58 years old. Multivariate logistic regression showed that the regular intake of carnation (OR [0.56], CI [0.37–0.85]), onion (OR [0.69], CI [0.52–0.92]), lemon (OR [0.68], CI [0.51–0.90]), and citrus fruits (OR [0.66], CI [0.50–0.89]) before infection were associated with a substantial reduction in COVID-19 severity (P<0.01). Also, the consumption of carnation (OR [0.55], CI [0.34–0.88]), lemon (OR [0.57], CI [0.42–0.78]), and citrus fruits (OR [0.61], CI [0.44–0.84]) were associated with a significant decrease in the frequency of COVID-19-induced hospitalization (P<0.01).

Conclusions: Regular consumption of carnation, lemon, and citrus fruits before infection was associated with better outcomes for COVID-19. Studies on other populations are required to confirm these findings.

Cell and Animal Models for SARS-CoV-2 Research

During the last two years following the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, development of potent antiviral drugs and vaccines has been a global health priority. In this context, the understanding of virus pathophysiology, the identification of associated therapeutic targets, and the screening of potential effective compounds have been indispensable advancements. It was therefore of primary importance to develop experimental models that recapitulate the aspects of the human disease in the best way possible. This article reviews the information concerning available SARS-CoV-2 preclinical models during that time, including cell-based approaches and animal models. We discuss their evolution, their advantages, and drawbacks, as well as their relevance to drug effectiveness evaluation.

Photobiomodulation Improves Serum Cytokine Response in Mild to Moderate COVID-19: The First Randomized, Double-Blind, Placebo Controlled, Pilot Study

Background

Because the major event in COVID-19 is the release of pre- and inflammatory cytokines, finding a reliable therapeutic strategy to inhibit this release, help patients manage organ damage and avoid ICU admission or severe disease progression is of paramount importance. Photobiomodulation (PBM), based on numerous studies, may help in this regard, and the present study sought to evaluate the effects of said technology on cytokine reduction.

Methods

This study was conducted in the 2nd half of 2021. The current study included 52 mild-to-moderately ill COVID-19, hospitalized patients. They were divided in two groups: a Placebo group and a PBM group, treated with PBM (620-635 nm light via 8 LEDs that provide an energy density of 45.40 J/cm2 and a power density of 0.12 W/cm2), twice daily for three days, along with classical approved treatment. 28 patients were in Placebo group and 24 in PBM group. In both groups, blood samples were taken four times in three days and serum IL-6, IL-8, IL-10, and TNF-α levels were determined.

Results

During the study period, in PBM group, there was a significant decrease in serum levels of IL-6 (-82.5% +/- 4, P&lt;0.001), IL-8 (-54.4% ± 8, P&lt;0.001), and TNF-α (-82.4% ± 8, P&lt;0.001), although we did not detect a significant change in IL-10 during the study. The IL-6/IL-10 Ratio also improved in PBM group. The Placebo group showed no decrease or even an increase in these parameters. There were no reported complications or sequelae due to PBM therapy throughout the study.

Conclusion

The major cytokines in COVID-19 pathophysiology, including IL-6, IL-8, and TNF-α, responded positively to PBM therapy and opened a new window for inhibiting and managing a cytokine storm within only 3-10 days.

Animal models for COVID-19: advances, gaps and perspectives

COVID-19, caused by SARS-CoV-2, is the most consequential pandemic of this century. Since the outbreak in late 2019, animal models have been playing crucial roles in aiding the rapid development of vaccines/drugs for prevention and therapy, as well as understanding the pathogenesis of SARS-CoV-2 infection and immune responses of hosts. However, the current animal models have some deficits and there is an urgent need for novel models to evaluate the virulence of variants of concerns (VOC), antibody-dependent enhancement (ADE), and various comorbidities of COVID-19. This review summarizes the clinical features of COVID-19 in different populations, and the characteristics of the major animal models of SARS-CoV-2, including those naturally susceptible animals, such as non-human primates, Syrian hamster, ferret, minks, poultry, livestock, and mouse models sensitized by genetically modified, AAV/adenoviral transduced, mouse-adapted strain of SARS-CoV-2, and by engraftment of human tissues or cells. Since understanding the host receptors and proteases is essential for designing advanced genetically modified animal models, successful studies on receptors and proteases are also reviewed. Several improved alternatives for future mouse models are proposed, including the reselection of alternative receptor genes or multiple gene combinations, the use of transgenic or knock-in method, and different strains for establishing the next generation of genetically modified mice.

SARS-CoV-2 and the Missing Link of Intermediate Hosts in Viral Emergence - What We Can Learn From Other Betacoronaviruses

The emergence of SARS-CoV-2 in 2019 has resulted in a global pandemic with devastating human health and economic consequences. The development of multiple vaccines, antivirals and supportive care modalities have aided in our efforts to gain control of the pandemic. However, the emergence of multiple variants of concern and spillover into numerous nonhuman animal species could protract the pandemic. Further, these events also increase the difficulty in simultaneously monitoring viral evolution across multiple species and predicting future spillback potential into the human population. Here, we provide historic context regarding the roles of reservoir and intermediate hosts in coronavirus circulation and discuss current knowledge of these for SARS-CoV-2. Increased understanding of SARS-CoV-2 zoonoses are fundamental for efforts to control the global health and economic impacts of COVID-19.

Bioactive components of different nasal spray solutions may defeat SARS-Cov2: repurposing and in silico studies

The recent outbreak "Coronavirus Disease 2019 (COVID-19)" is caused by fast-spreading and highly contagious severe acute respiratory syndrome coronavirus 2 (SARS-CoV2). This virus enters into the human respiratory system by binding of the viral surface spike glycoprotein (S-protein) to an angiotensin-converting enzyme2 (ACE2) receptor that is found in the nasal passage and oral cavity of a human. Both spike protein and the ACE2 receptor have been identified as promising therapeutic targets to develop anti-SARS-CoV2 drugs. No therapeutic drugs have been developed as of today except for some vaccines. Therefore, potent therapeutic agents are urgently needed to combat the COVID-19 infections. This goal would be achieved only by applying drug repurposing and computational approaches. Thus, based on drug repurposing approach, we have investigated 16 bioactive components (1-16) from different nasal spray solutions to check their efficacies against human ACE2 and SARS-CoV2 spike proteins by performing molecular docking and molecular dynamic (MD) simulation studies. In this study, three bioactive components namely ciclesonide (8), levocabastine (13), and triamcinolone acetonide (16) have been found as promising inhibitory agents against SARS-CoV2 spike and human ACE2 receptor proteins with excellent binding affinities, comparing to reference drugs such as nafamostat, arbidol, losartan, and benazepril. Furthermore, MD simulations were performed (triplicate) for 100 ns to confirm the stability of 8, 13, and 16 with said protein targets and to compute MM-PBSA-based binding-free energy calculations. Thus, bioactive components 8, 13, and 16 open the door for researchers and scientist globally to investigate them against SARS-CoV2 through in vitro and in vivo analysis.

COVID-19 vaccination efficacy in numbers including SARS-CoV-2 variants and age comparison: a meta-analysis of randomized clinical trials

Background

New vaccines are being developed to fight the ongoing COVID-19 pandemic. In our study we compared the efficacy of COVID-19 vaccines to prevent COVID-19-related infections and mortality.

Methods

17 randomized clinical trials of COVID-19 vaccines were included after search in databases. We compared COVID-19 vaccines based on symptomatic and severe infections, number of deaths and hospitalizations related to COVID-19. Also, we analyzed the efficacy of COVID-19 against different variants of SARS-CoV-2 as well as according to different age groups. Random effects model using Mantel–Haenzeal method was used to pool relative risk (RR).

Results

Our meta-analysis shows that full vaccination could decrease not only the risk of symptomatic or severe COVID-19, the risk of hospitalization and death caused by COVID-19. COVID-19 vaccines were also effective against variants of SARS-CoV-2 (RR = 0.36; 95% CI [0.25; 0.53], p < 0.0001). However, efficacy of vaccination varied in COVID-19 variant-dependent manner. Moreover, the analysis in different age groups showed that COVID-19 vaccines had the similar results: the risk was slightly lower in adults compared to elderly cohort \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$(\ge$$\end{document}(≥ 65 years): (RR = 0.16, 95% CI [0.11; 0.23]) and (RR = 0.19, 95% CI [0.12; 0.30]), respectively.

Conclusions

Data obtained from clinical trials of COVID-19 vaccines looks promising, in order to fully investigate efficacy of the vaccines further clinical examination is required especially considering new SARS-CoV-2 variants.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12941-022-00525-3.

Comparative changes in emergency department patient attendance at the pediatric emergency hospital during the first wave between 2019 and 2020

The COVID-19 pandemic changed the pattern of patient attendance at healthcare facilities. We describe the comparative changes in the attendance of pediatric patients at the Emergency Department of the Pediatric Emergency Hospital of Lima, Peru, between epidemiological weeks 10 to 48 of 2019 and 2020. Sociodemographic data, patient condition, type of insurance and diagnosis grouped according to ICD-10 code were analyzed. We found a 48.2% reduction in the number of visits in 2020 when compared to 2019, and a five-fold increase in the number of visits from localities other than Metropolitan Lima. Likewise, the probability of diagnosis of "infectious and parasitic diseases" increased by 27% and the probability of diagnosis of "diseases of the respiratory system" decreased by 61%.

Omicron and vaccine booster dose – an update

Mutations in coronavirus is not unheard off. The variant, Omicron B.1.1.529 has overall 50 mutations and is considered as a variant of concern. Though the new variant has shown changes throughout its genome, S gene changes predominate. Significant changes in the S encoding gene, S gene, influences not only the transmissibility properties of SARS-CoV-2 but also the efficacy of existing vaccines. Increased transmissibility and ability of this variant to evade host immune responses conferred either due to past infections or due to vaccination driving increase in number of infections. However, the severity of the infections is low in comparison to its predecessors. A meta-analysis of ten studies analyzing the effect of COVID-19 vaccine booster dose, it was found studies report 10-to-42-fold increase in omicron neutralization. COVID appropriate behaviors, if followed rigidly can bring a meaningful change in the viral spread and resultant health impacts.

Human ACE2 Polymorphisms from Different Human Populations Modulate SARS-CoV-2 Infection

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in over 6 million deaths worldwide. The high variability in COVID-19 symptoms remains one of the most interesting mysteries of the pandemic. Genetic and environmental factors are likely to be key determinants of COVID-19 symptomatology. Here, we explored ACE2 as a genetic determinant for SARS-CoV-2 infection and COVID-19 symptomatology. Each human genome encodes two alleles of ACE2, which encodes the cell entry receptor for SARS-CoV-2. Here, we determined whether naturally occurring human ACE2 (hACE2) polymorphisms in the human population affect SARS-CoV-2 infection and the severity of COVID-19 symptoms. ACE2 variants S19P, I21V, E23K, K26R, K31R, N33I, H34R, E35K, and T92I showed increased virus infection compared to wild-type ACE2; thus, these variants could increase the risk for COVID-19. In contrast, variants D38V, Y83H, I468V, and N638S showed reduced infection, indicating a potential protective effect. hACE2 variants K26R and T92I increased infection by three-fold without changing the levels of ACE2 on the surface of the cells, suggesting that these variants may increase the risk of severe COVID-19. On the contrary, hACE2 variants D38V and Y83H decreased SARS-CoV-2 infection by four- and ten-fold, respectively, without changing surface expression, suggesting that these variants may protect against severe COVID-19. Remarkably, all protective hACE2 Polymorphisms were found almost exclusively in Asian populations, which may provide a partial explanation for the low COVID-19 mortality rates in Asian countries. Thus, hACE2 polymorphisms may modulate susceptibility to SARS-CoV-2 in the host and partially account for the differences in severity of COVID-19 among different ethnic groups.

Insighting isatin derivatives as potential antiviral agents against NSP3 of COVID-19

The world is now facing intolerable damage in all sectors of life because of the deadly COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2. The discovery and development of anti-SARS-CoV-2 drugs have become pragmatic in the time needed to fight against this pandemic. The non-structural protein 3 is essential for the replication of transcriptase complex (RTC) and may be regarded as a possible target against SARS-CoV-2. Here, we have used a comprehensive in silico technique to find potent drug molecules against the NSP3 receptor of SARS-CoV-2. Virtual screening of 150 Isatin derivatives taken from PubChem was performed based on their binding affinity estimated by docking simulations, resulting in the selection of 46 ligands having binding energy greater than -7.1 kcal/mol. Moreover, the molecular interactions of the nine best-docked ligands having a binding energy of ≥ -8.5 kcal/mol were analyzed. The molecular interactions showed that the three ligands (S5, S16, and S42) were stabilized by forming hydrogen bonds and other significant interactions. Molecular dynamic simulations were performed to mimic an in vitro protein-like aqueous environment and to check the stability of the best three ligands and NSP3 complexes in an aqueous environment. The binding energy of the S5, S16, and S42 systems obtained from the molecular mechanics Poisson-Boltzmann surface area also favor the system's stability. The MD and MM/PBSA results explore that S5, S16, and S42 are more stable and can be considered more potent drug candidates against COVID-19 disease.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11696-022-02298-7.

Hematological- and Immunological-Related Biomarkers to Characterize Patients with COVID-19 from Other Viral Respiratory Diseases

COVID-19 has overloaded health system worldwide; thus, it demanded a triage method for an efficient and early discrimination of patients with COVID-19. The objective of this research was to perform a model based on commonly requested hematological variables for an early featuring of patients with COVID-19 form other viral pneumonia. This investigation enrolled 951 patients (mean of age 68 and 56% of male) who underwent a PCR test for respiratory viruses between January 2019 and January 2020, and those who underwent a PCR test for detection of SARS-CoV-2 between February 2020 and October 2020. A comparative analysis of the population according to PCR tests and logistic regression model was performed. A total of 10 variables were found for the characterization of COVID-19: age, sex, anemia, immunosuppression, C-reactive protein, chronic obstructive pulmonary disease, cardiorespiratory disease, metastasis, leukocytes and monocytes. The ROC curve revealed a sensitivity and specificity of 75%. A deep analysis showed low levels of leukocytes in COVID-19-positive patients, which could be used as a primary outcome of COVID-19 detection. In conclusion, this investigation found that commonly requested laboratory variables are able to help physicians to distinguish COVID-19 and perform a quick stratification of patients into different prognostic categories.

Structural, genomic information and computational analysis of emerging coronavirus (SARS-CoV-2)

Background

The emerging viral pandemic worldwide is associated with a novel coronavirus, SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). This virus is said to emerge from its epidemic center in Wuhan, China, in 2019. Coronaviruses (CoVs) are single-stranded, giant, enveloped RNA viruses that come under the family of coronaviridae and order Nidovirales which are the crucial pathogens for humans and other vertebrates.

Main body

Coronaviruses are divided into several subfamilies and genera based on the genomic structure and phylogenetic relationship. The name corona is raised due to the presence of spike protein on the envelope of the virus. The structural and genomic study revealed that the total genome size of SARS-CoV-2 is from 29.8 kb to 29.9 kb. The spike protein (S) is a glycoprotein that attaches to the receptor of host cells for entry into the host cell, followed by the attachment of virus RNA to the host ribosome for translation. The phylogenetic analysis of SARS-CoV-2 revealed the similarity (75-88%) with bat SARS-like coronavirus.

Conclusion

The sign and symptoms of novel severe acute respiratory syndrome coronavirus 2 are also discussed in this paper. The worldwide outbreak and prevention from severe acute respiratory syndrome coronavirus 2 are overviewed in the present article. The latest variant of coronavirus and the status of vaccines are also overviewed in the present article.

Magnetofluid-Integrated Multicolor Immunochip for Visual Analysis of Neutralizing Antibodies to SARS-CoV-2 Variants

The global spread of SARS-CoV-2 virus has severely affected human health, life, and work. Vaccine immunization is considered to be an effective means to protect the body from infection. Therefore, timely analysis of the antibody level is helpful to identify people with low immune response or attenuated antibodies so as to carry out targeted and precise vaccine booster immunization. Herein, we develop a magnetofluid-integrated multicolor immunochip, as a sample-to-answer system in a fully enclosed space, for visual analysis of neutralizing antibodies of SARS-CoV-2. Generally, this chip adopts an innovative three-dimensional two-phase system that utilizes mineral oil to block the connection between reagent wells in the vertical direction and provides a wide interface for rapid and nondestructive shuttle of magnetic beads during the immunoassay. In order to obtain visualized signal output, gold nanorods with a size-dependent color effect are used as the colorful chromogenic substrates for evaluation of the antibody level. Using this chip, the neutralizing antibodies were successfully detected in vaccine-immunized volunteers with 83.3% sensitivity and 100% specificity. Furthermore, changes in antibody levels of the same individual over time were also reflected by the multicolor assay. Overall, benefiting from simple operation, airtight safety, and nonrequirement of external equipment, this platform can provide a new point-of-care testing strategy for alleviating the shortage of medical resources and promoting epidemic control in underdeveloped areas.

Preclinical Assessment of IgY Antibodies Against Recombinant SARS-CoV-2 RBD Protein for Prophylaxis and Post-Infection Treatment of COVID-19

Within the framework of the current COVID-19 pandemic, there is a race against time to find therapies for the outbreak to be controlled. Since vaccines are still tedious to develop and partially available for low-income countries, passive immunity based on egg-yolk antibodies (IgY) is presented as a suitable approach to preclude potential death of infected patients, based on its high specificity/avidity/production yield, cost-effective manufacture, and ease of administration. In the present study, IgY antibodies against a recombinant RBD protein of SARS-CoV-2 were produced in specific-pathogen-free chickens and purified from eggs using a biocompatible method. In vitro immunoreactivity was tested, finding high recognition and neutralization values. Safety was also demonstrated prior to efficacy evaluation, in which body weight, kinematics, and histopathological assessments of hamsters challenged with SARS-CoV-2 were performed, showing a protective effect administering IgY intranasally both as a prophylactic treatment or a post-infection treatment. The results of this study showed that intranasally delivered IgY has the potential to both aid in prevention and in overcoming COVID-19 infection, which should be very useful to control the advance of the current pandemic and the associated mortality.

Inhibitory effect of compounds extracted from Monochoria hastata (L.) Solms on SARS-CoV-2 main protease: An insight from molecular docking and MD-simulation studies

Using molecular docking and other studies, 20 compounds extracted from Monochoria hastata (L.) Solms were screened, and their inhibitory efficiency examined against main protease (3CLpro) of SARS CoV-2. All the compounds were found to binding with 3CLpro through van der Waals and electrostatic forces of attractions. Among them, Azelaic dihydrazide (ADZ) was found to have the highest docking score. 3CLpro-ADZ complex was studied by MD simulation. ADZ was found to disrupt the structure of 3CLpro after 2 ns. RMSD and RMSF analysis along with sequence and binding energy analysis suggest that ADZ can be a potential drug against SARS CoV-2.

COVID-19: Rapid prototyping and production of face shields via flat, laser-cut, and 3D-printed models

The use of personal protective equipment (PPE) has become essential to reduce the transmission of coronavirus disease 2019 (COVID-19) as it prevents the direct contact of body fluid aerosols expelled from carriers. However, many countries have reported critical supply shortages due to the spike in demand during the outbreak in 2020. One potential solution to ease pressure on conventional supply chains is the local fabrication of PPE, particularly face shields, due to their simplistic design. The purpose of this paper is to provide a research protocol and cost implications for the rapid development and manufacturing of face shields by individuals or companies with minimal equipment and materials. This article describes a best practice case study in which the establishment of a local manufacturing hub resulted in the swift production of 12,000 face shields over a seven-week period to meet PPE shortages in the North-West region of Ireland. Protocols and processes for the design, materials sourcing, prototyping, manufacturing, and distribution of face shields are described. Three types of face shields were designed and manufactured, including Flat, Laser-cut, and 3D-printed models. Of the models tested, the Flat model proved the most cost-effective (€0.51/unit), while the Laser-cut model was the most productive (245 units/day). The insights obtained from this study demonstrate the capacity for local voluntary workforces to be quickly mobilised in response to a healthcare emergency, such as the COVID-19 pandemic.

Evaluation of SARS-CoV-2 in Indoor Air of Sina and Shahid Beheshti Hospitals and Patients' Houses

Side by side air sampling was conducted using a PTFE filter membrane as dry sampler and an impinger containing a suitable culture medium as a wet sampler. Most of the samples were collected from two hospitals and few air samples were collected from private houses of non-hospitalized confirmed COVID-19 patients. The collected air samples were analyzed using RT-PCR. The results indicated that all air samples collected from the hospitals were PCR negative for SARS-CoV-2. While two of four air samples collected from the house of non-hospitalized patients were PCR positive. In this study, most of the hospitalized patients had oxygen mask and face mask, and hence this may be a reason for our negative results regarding the presence of SARS-CoV-2 in indoor air of the hospitals, while non-hospitalized patients did not wear oxygen and protective face masks in their houses. Moreover, a very high concentration of particles in the size range of droplet nuclei (< 5 µm) was identified compared to particles in the size range of respiratory droplets (> 5-10 µm) in the areas where patients were hospitalized. It can be concluded that using face mask by patients can prevent the release of viruses into the indoor air, even in hospitals with a high density of patients.

Success of Current COVID-19 Vaccine Strategies vs. the Epitope Topology of SARS-CoV-2 Spike Protein-Receptor Binding Domain (RBD): A Computational Study of RBD Topology to Guide Future Vaccine Design

Coronavirus disease-2019 (COVID-19) is a pandemic with a high morbidity rate occurring over recent years. COVID-19 is caused by the severe acute respiratory syndrome causing coronavirus type-2 (SARS-CoV-2). COVID-19 not only challenged mankind but also gave scope to the evolution of various vaccine design technologies. Although these vaccines protected and saved many lives, with the emerging viral strains, some of the strains may pose a threat to the currently existing vaccine design that is primarily based on the wild type spike protein of SARS-CoV-2. To evaluate the risk involved from such mutant viral strains, we performed a systematic in silico amino acid substitution of critical residues in the receptor binding domain (RBD) of the spike protein. Our molecular modeling analysis revealed significant topological changes in the RBD of spike protein suggesting that they could potentially contribute to the loss of antigen specificity for the currently existing therapeutic antibodies/vaccines, thus posing a challenge to the current vaccine strategies that are based on wild type viral spike protein epitopes. The structural deviations discussed in this article should be considered carefully in the future vaccine design.

Molecular and Clinical Investigation of COVID-19: From Pathogenesis and Immune Responses to Novel Diagnosis and Treatment

The coronavirus-related severe acute respiratory syndrome (SARS-CoV) in 2002/2003, the Middle East respiratory syndrome (MERS-CoV) in 2012/2013, and especially the current 2019/2021 severe acute respiratory syndrome-2 (SARS-CoV-2) negatively affected the national health systems worldwide. Different SARS-CoV-2 variants, including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and recently Omicron (B.1.1.529), have emerged resulting from the high rate of genetic recombination and S1-RBD/S2 mutation/deletion in the spike protein that has an impact on the virus activity. Furthermore, genetic variability in certain genes involved in the immune system might impact the level of SARS-CoV-2 recognition and immune response against the virus among different populations. Understanding the molecular mechanism and function of SARS-CoV-2 variants and their different epidemiological outcomes is a key step for effective COVID-19 treatment strategies, including antiviral drug development and vaccine designs, which can immunize people with genetic variabilities against various strains of SARS-CoV-2. In this review, we center our focus on the recent and up-to-date knowledge on SARS-CoV-2 (Alpha to Omicron) origin and evolution, structure, genetic diversity, route of transmission, pathogenesis, new diagnostic, and treatment strategies, as well as the psychological and economic impact of COVID-19 pandemic on individuals and their lives around the world.

Chest Computed Tomography Is an Efficient Method for Initial Diagnosis of COVID-19: An Observational Study

Coronavirus disease (COVID-19) is an infectious disease that can lead to pneumonia, pulmonary oedema, acute respiratory distress syndrome, multiple organ and system dysfunction, and death. This study aimed to verify the efficacy of chest computed tomography (CT) for the initial diagnosis of COVID-19. This observational, retrospective, cross-sectional study included 259 individuals who underwent clinical evaluation, blood collection, chest CT, and a reverse transcription polymerase chain reaction (RT-PCR) diagnostic test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during their course of treatment at a reference hospital in Belém, Pará, Brazil between April and June 2020. Inclusion criteria were flu-like symptoms in adults of both sexes. Individuals with an inconclusive COVID-19 molecular test or who had artifacts in the chest CT images were excluded. Parametric data were analyzed using Student-t-test and non-parametric data were analyzed using average test and Fisher exact test. Participants were divided into two groups: Group 1 (COVID-19 positive), n = 211 (124 males, 87 females), 51.8 ± 17.9 years old and Group 2 (COVID-19 negative), n = 48 (22 males, 26 females), 47.6 ± 18.6 years old. Most frequent symptoms were cough [Group 1 n = 199 (94%)/Group 2 n = 46 (95%)], fever [Group 1 n = 154 (72%)/Group 2 n = 28 (58%)], myalgia [Group 1 n = 172 (81%)/Group 2 n = 38 (79%)], dyspnoea [Group 1 n = 169 (80%) / Group 2 n = 37 (77%)], headache [Group 1 n = 163 (77%)/Group 2 n = 32 (66%)], and anosmia [Group 1 n = 154 (73%)/Group 2 n = 29 (60%)]. Group 1 had a higher proportion of ground-glass opacity [Group 1 n = 175 (83%)/Group 2 n = 24 (50%), 0.00], vascular enhancement sign [Group 1 n = 128 (60%)/Group 2 n = 15 (31%), 0.00], septal thickening [Group 1 n = 99 (47%)/Group 2 n = 13 (27%), 0.01], crazy-paving pattern [Group 1 n = 98 (46%) / Group 2 n = 13 (27%), 0.01], consolidations [Group 1 n = 92 (43%)/Group 2 n = 8 (16%), 0.00], and CO-RADS 4 and 5 [Group 1 n = 163 (77.25%)/Group 2 n = 24 (50%), 0.00] categories in chest CT. Chest CT, when available, was found to be an efficient method for the initial diagnosis and better management of individuals with COVID-19.

Furin and TMPRSS2 Resistant Spike Induces Robust Humoral and Cellular Immunity Against SARS-CoV-2 Lethal Infection

An effective COVID-19 vaccine against broad SARS-CoV-2 variants is still an unmet need. In the study, the vesicular stomatitis virus (VSV)-based vector was used to express the SARS-CoV-2 Spike protein to identify better vaccine designs. The replication-competent of the recombinant VSV-spike virus with C-terminal 19 amino acid truncation (SΔ19 Rep) was generated. A single dose of SΔ19 Rep intranasal vaccination is sufficient to induce protective immunity against SARS-CoV-2 infection in hamsters. All the clones isolated from the SΔ19 Rep virus contained R682G mutation located at the Furin cleavage site. An additional S813Y mutation close to the TMPRSS2 cleavage site was identified in some clones. The enzymatic processing of S protein was blocked by these mutations. The vaccination of the R682G-S813Y virus produced a high antibody response against S protein and a robust S protein-specific CD8+ T cell response. The vaccinated animals were protected from the lethal SARS-CoV-2 (delta variant) challenge. The S antigen with resistance to enzymatic processes by Furin and TMPRSS2 will provide better immunogenicity for vaccine design.

SARS-CoV-2 antibody seroprevalence rates among Egyptian blood donors around the third wave: Cross-sectional study

Background

Seroprevalence studies may provide a more representative situation of the disease burden and population-level immunity in a country.

Aim

The aim of this study was to determine the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies among asymptomatic blood donors attending the Cairo University blood bank services at various points in time around the third wave.

Methods

This cross-section study included 3058 eligible blood donors, representing a demographically and socially heterogeneous healthy population and categorized as: Group 1, 954 donors in the period from March 20 to 30/2021; Group 2, 990 donors in the period from June 3 to 10/2021. These two groups were tested for IgG against SARS-CoV-2 nucleocapsid antigen (NC) to detect qualitative reactivity. Group 3, 1114 donors in the period from July 20 to 30/2021 were tested by the SARS-CoV-2 IgG II Quant assay for the quantitative detection of IgG antibodies, including neutralizing antibodies (antispike antibodies).

Results

Donors' age ranged between 18 and 59 (mean 33.9 ± 9) years. There was no significant correlation between seroprevalence and gender, area of residence, ABO or Rh blood types, and occupation or education. Antibody prevalence was found to be 13.2% in Group 1, 19.2% in Group 2 (overall 16.2%), and 66% in Group 3. There were only 49 included cases vaccinated against COVID-19.

Conclusion

We concluded that the significant increasing trend in seroprevalence rates during the third wave, March, June, and July, in Egypt, reflects a high cumulative incidence of seroconversion that mirrored the epidemic curve in its rise, fall, and nadir.

mRNA vaccines for COVID-19 and diverse diseases

Since its outbreak in late 2019, the novel coronavirus disease 2019 (COVID-19) has spread to every continent on the planet. The global pandemic has affected human health and socioeconomic status around the world. At first, the global response to the pandemic was to isolate afflicted individuals to prevent the virus from spreading, while vaccine development was ongoing. The genome sequence was first presented in early January 2020, and the phase I clinical trial of the vaccine started in March 2020 in the United States using novel lipid-based nanoparticle (LNP), encapsulated with mRNA termed as mRNA-1273. Till now, various mRNA-based vaccines are in development, while one mRNA-based vaccine got market approval from US-FDA for the prevention of COVID-19. Previously, mRNA-based vaccines were thought to be difficult to develop, but the current development is a significant accomplishment. However, widespread production and global availability of mRNA-based vaccinations to combat the COVID-19 pandemic remains a major challenge, especially when the mutations continually occur on the virus (e.g., the recent outbreaks of Omicron variant). This review elaborately discusses the COVID-19 pandemic, the biology of SARS-CoV-2 and the progress of mRNA-based vaccines. Moreover, the review also highlighted a detailed description of mRNA delivery technologies and the application potential in controlling other life-threatening diseases. Therefore, it provides a comprehensive view and multidisciplinary insights into mRNA therapy for broader audiences.

Probing the Immune System Dynamics of the COVID-19 Disease for Vaccine Designing and Drug Repurposing Using Bioinformatics Tools

The pathogenesis of COVID-19 is complicated by immune dysfunction. The impact of immune-based therapy in COVID-19 patients has been well documented, with some notable studies on the use of anti-cytokine medicines. However, the complexity of disease phenotypes, patient heterogeneity and the varying quality of evidence from immunotherapy studies provide problems in clinical decision-making. This review seeks to aid therapeutic decision-making by giving an overview of the immunological responses against COVID-19 disease that may contribute to the severity of the disease. We have extensively discussed theranostic methods for COVID-19 detection. With advancements in technology, bioinformatics has taken studies to a higher level. The paper also discusses the application of bioinformatics and machine learning tools for the diagnosis, vaccine design and drug repurposing against SARS-CoV-2.

In Silico Analysis Prediction of B-Cell Epitope as a Vaccine Candidate for SARS-CoV-2 B.1.617.2 (Delta) Variant

Background: The COVID-19 pandemic by SARS-CoV-2 has caused many losses. One way to prevent the spread of this virus is to get vaccinated. However, the latest SARS-CoV-2 variants, including variant B.1.617.2 (Delta) are doubtful to be inhibited by existing vaccines because of mutations. Therefore, we need a new vaccine candidate that is effective against this SARS-CoV-2 variant. Through an immunoinformatics approach with various software and analysis websites, vaccine candidates can be predicted in a short time.Objective: Identity, analyze, obtain, and confirm the selected B-cell epitope sequence that can be used as a vaccine candidate for the SARS-CoV-2 B.1.617.2 (Delta) variant.Methods: This research was conducted by isolating the amino acid peptide sequence in the SARS-CoV-2 B.1.617.2 (Delta) variant protein spike from the Protein Data Bank which is suspected to be an immunogenic epitope and can be used as a vaccine candidate. A Series of tests were carried out such as antigenicity, toxicity, allergenicity, and BLAST® protein to ensure that this vaccine candidate is safe for later application into the human body. The next stage is a conservation analysis to see its potential by comparing it with the SARS-CoV-2 Delta (B.1.617.2) variant spike protein sequence in Indonesia. The study ended by mapping amino acid peptides to the SARS-CoV-2 Delta (B.1.617.2) variant spike protein using the Biovia Discovery Studio Visualizer v21.1.0.20298 2020 software to ensure that the selected sequences were epitope.Results: From the five amino acid peptides that have been isolated, the FTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFT epitope sequence has good results than the others. It is probable an antigen, non-toxic, non-allergen, and non-homolog to the human body protein.Conclusion: Based on this in silico study, it was found that the FTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFT epitope sequence was the best to be used as a vaccine candidate of SARS-CoV-2 B.1.617.2 (Delta) variant.Keywords: SARS-CoV-2 B.1.617.2 (Delta) variant, B-cell epitope, vaccine, in silico, immunoinformatics.

The Assessment of COVID-19 Vulnerability Risk for Crisis Management

The subject of this article is to determine COVID-19 vulnerability risk and its change over time in association with the state health care system, turnover, and transport to support the crisis management decision-making process. The aim was to determine the COVID-19 Vulnerability Index (CVI) based on the selected criteria. The risk assessment was carried out with methodology that includes the application of multicriteria analysis and spatiotemporal aspect of available data. Particularly the Spatial Multicriteria Analysis (SMCA) compliant with the Analytical Hierarchy Process (AHP), which incorporated selected population and environmental criteria were used to analyse the ongoing pandemic situation. The influence of combining several factors in the pandemic situation analysis was illustrated. Furthermore, the static and dynamic factors to COVID-19 vulnerability risk were determined to prevent and control the spread of COVID-19 at the early stage of the pandemic situation. As a result, areas with a certain level of risk in different periods of time were determined. Furthermore, the number of people exposed to COVID-19 vulnerability risk in time was presented. These results can support the decision-making process by showing the area where preventive actions should be considered.

An overview of post COVID sequelae

After healing from COVID-19, patients often experience a slew of symptoms known as post COVID-19 sequelae. Despite the fact that the SARS-CoV-2 pandemic is still ongoing, post-Covid-19 syndrome is already a difficult problem to address: long-term multiorgan sequelae, while frequently described, have yet to be systematized. As a result, post-Covid-19 syndrome can have a major influence on surviving patients' working capacity as well as their personal lives. The clinical spectrum and long-term course of this clinical entity must be better understood. Post-Covid syndrome affects a wide spectrum of individuals (16-87%), with pneumological and cognitive symptoms being the most common. Pulmonary fibrosis was the most common organic consequence seen in post-Covid patients. In conclusion, post-Covid-19 syndrome can have a major impact on the health of survivors. Working-age patients should seek rehabilitation and follow-up in interdisciplinary rehabilitation programmes. Given the pandemic's global extent, it's obvious that COVID-19-related healthcare demands will continue to climb for the foreseeable future. For COVID-19 survivors' long-term mental and physical health, present outpatient infrastructure will be utilised, scalable healthcare models will be built, and cross-disciplinary collaboration will be required.

Factors Associated with Death of Covid-19 Patients: Case Series

This aim of this study was to identify potential factors associated with survival in patients with coronavirus disease 2019 (COVID- 19). This study was designed as a case series. It included patients hospitalized in Clinical Centre Kragujevac between March 10, 2020, and June 15, 2020, due to COVID-19. Variables with significant influence on the cure of patients were identified by multivariate logistic regression. A total of 234 patients were included. The average age of the patients was 57.2 ± 15.8 years. Thirty-five patients died (15.0%) and 199 (85.0%) were discharged as completely cured and with the sustained virological response.

The study variables with significant influence (expressed as odds ratio – OR) on cure of COVID-19 patients after adjustment for effects of other variables were: stay in an intensive care unit – ICU (OR = 0.007; 95% confidence interval – CI 0.001 – 0.086; p = 0.000), previous hospitalization (OR = 7.802; 95% CI 1.198 – 50.924; p = 0.032), increased body temperature on admission (OR = 0.004; 95% CI 0.000 – 0.771; p = 0.040), higher score of the Charlson Comorbidity Index (OR = 0.428; 95% CI 0.235 – 0.780; p = 0.006), and increased values of C-reactive protein (CRP) serum level (OR = 0.978; 95% CI 0.966 – 0.990; p = 0.000). In conclusion, clinicians should pay attention to patients with high body temperature at admission, presence of multiple comorbidities, high CRP, and patients who stay in an ICU, considering that they could be at risk for fatal outcome.

Network Pharmacology Study to Elucidate the Key Targets of Underlying Antihistamines against COVID-19

Antihistamines have potent efficacy to alleviate COVID-19 (Coronavirus disease 2019) symptoms such as anti-inflammation and as a pain reliever. However, the pharmacological mechanism(s), key target(s), and drug(s) are not documented well against COVID-19. Thus, we investigated to decipher the most significant components and how its research methodology was utilized by network pharmacology. The list of 32 common antihistamines on the market were retrieved via drug browsing databases. The targets associated with the selected antihistamines and the targets that responded to COVID-19 infection were identified by the Similarity Ensemble Approach (SEA), SwissTargetPrediction (STP), and PubChem, respectively. We described bubble charts, the Pathways-Targets-Antihistamines (PTA) network, and the protein–protein interaction (PPI) network on the RPackage via STRING database. Furthermore, we utilized the AutoDock Tools software to perform molecular docking tests (MDT) on the key targets and drugs to evaluate the network pharmacological perspective. The final 15 targets were identified as core targets, indicating that Neuroactive ligand–receptor interaction might be the hub-signaling pathway of antihistamines on COVID-19 via bubble chart. The PTA network was constructed by the RPackage, which identified 7 pathways, 11 targets, and 30 drugs. In addition, GRIN2B, a key target, was identified via topological analysis of the PPI network. Finally, we observed that the GRIN2B-Loratidine complex was the most stable docking score with −7.3 kcal/mol through molecular docking test. Our results showed that Loratadine might exert as an antagonist on GRIN2B via the neuroactive ligand–receptor interaction pathway. To sum up, we elucidated the most potential antihistamine, a key target, and a key pharmacological pathway as alleviating components against COVID-19, supporting scientific evidence for further research.

Cross-reactive cellular, but not humoral, immunity is detected between OC43 and SARS-CoV-2 NPs in people not infected with SARS-CoV-2: Possible role of cTFH cells

Multiple questions about SARS-CoV-2 humoral and cellular immunity remain unanswered. One key question is whether preexisting memory T or B cells, specific for related coronaviruses in SARS-CoV-2-unexposed individuals, can recognize and suppress COVID-19, but this issue remains unclear. Here, we demonstrate that antibody responses to SARS-CoV-2 antigens are restricted to serum samples from COVID-19 convalescent individuals. In contrast, cross-reactive T cell proliferation and IFN-γ production responses were detected in PBMCs of around 30% of donor samples collected prepandemic, although we found that these prepandemic T cell responses only elicited weak cT_FH activation upon stimulation with either HCoV-OC43 or SARS-CoV-2 NP protein. Overall, these observations confirm that T cell cross-reactive with SARS-CoV-2 antigens are present in unexposed people, but suggest that the T cell response to HCoV-OC43 could be deficient in some important aspects, like T_FH expansion, that might compromise the generation of cross-reactive T_FH cells and antibodies. Understanding these differences in cellular responses may be of critical importance to advance in our knowledge of immunity against SARS-CoV-2.

The Implementation of the European Green Deal Strategy as a Challenge for Energy Management in the Face of the COVID-19 Pandemic

This article aims to present changes in the use of electricity by service companies, resulting from regulations within the framework of increasing energy efficiency from the perspective of the implementation of the European Green Deal strategy. To achieve the above goal, the following research question was formulated: to what extent did the COVID-19 pandemic affect the implementation of energy transformation and electricity consumption among the surveyed group of recipients? It should be noted that, so far in the global environment, more and more electricity has been used every year, and this tendency is still continuous and growing. Therefore, in European Union countries, measures have been taken to balance demand and its rational use, resulting from the implementation of the European Green Deal strategy. According to the strategic goal of the indicated policy, EU countries are obliged to implement a sequence of actions enabling their transformation into a modern, resource-efficient, and competitive economy. In particular, the strategy aims to achieve three main goals: 1. Achieving climate neutrality by reducing net greenhouse gas emissions to zero in 2050; 2. Decoupling economic growth from the consumption of natural resources; and 3. Striving for an equal standard of living in all countries. Therefore, the behavior of individual countries should focus on providing the required amount of energy to ensure socioeconomic growth while reducing pollution and environmental devastation caused by traditional methods of energy production and use. There are numerous talks and debates about the defined tasks and mechanisms leading to the achievement of the indicated goals, in which hardly any mention is made of the methods of monitoring the progress and evaluation of individual projects at the stage of building a new green deal. This study aims to fill the research gap observed in the current state of knowledge on energy management in EU countries from the perspective of the European Green Deal strategy and changes in its management resulting from the conditions of the COVID-19 pandemic. Therefore, in line with the aim of the article: 1. Factors influencing electricity consumption in service enterprises operating in EU countries were indicated; 2. Energy consumption variability in these entities was determined; and 3. The correlation between electricity consumption and GDP growth in the service sector located in EU countries was indicated. Therefore, a hybrid research method was used to analyze the data obtained from the databases of Eurostat and Statistics Poland, which consisted of the following analyses: diagnostic-descriptive, main components, and wavelet transform. Based on the conducted research, it should be concluded that energy consumption among service companies operating in the EU market is conditioned by three sources of causes along with the relevant consumption factors. The first group includes energy and technical premises, along with technological determinants. The second is shaped by financial and economic motives, which include socioeconomic factors. The third group is related to environmental sources represented by the natural environment and geographic and meteorological factors. The increase in electricity consumption in service enterprises is related to the average GDP growth of EU countries following a two-way cause-and-effect relationship implemented until 2019. Nevertheless, since 2020, there has been a noticeable decrease in energy consumption by 14.01% by service entities, which results from the limitations caused by the COVID-19 pandemic and the implementation of the European Green Deal strategy. Meanwhile, the structure of electricity consumption growth was dominated by industrial enterprises (increased by 37.7%) and individual consumers (increased by 7.8%). The results of the research may motivate the managers of EU countries and enterprises to analyze the factors of energy consumption, its variability, and dependence on economic growth, which contribute to determining the forecast of future energy demand, in connection with the ongoing energy transformation resulting from the implementation of the European Green Deal strategy, and economic slowdown caused by the COVID-19 pandemic. The issues presented in this article are an attempt to fill the gap indicating practical experience related to the process of electricity management and management in the political, economic, and technological dimensions from the perspective of implementing the European Green Deal strategy and the conditions resulting from the COVID-19 pandemic.

Life cycle environmental impacts of disposable medical masks

A massive increase in the use and production of masks worldwide has been seen in the current COVID-19 pandemic, which has contributed to reducing the transmission of the virus globally. This paper aims to evaluate the life cycle environmental impacts of disposable medical masks to identify the life cycle stages that cause the highest impact on the environment. A further goal is to estimate the total environmental impacts at the global level in 2020. The inventory data was constructed directly from the industry. The system boundary of the study is from cradle to grave comprising raw material extraction and processing, production, packaging, distribution, use, and disposal as well as transport and waste management along the supply chain. Eleven environmental impacts have been estimated. The results suggest that the global warming potential of a disposable medical mask is 0.02 g CO2-eq. for which the main contributor is the raw material supply (40.5%) followed by the packaging (30.0%) and production (15.5%). Sensitivity analysis was carried out to test the environmental impacts. In total, 52 billion disposable medical masks used worldwide consumes 22 TJ of energy in 2020. The global warming potential of disposable medical masks supplied in a year of the COVID-19 pandemic is 1.1 Mt CO2 eq. This paper assessed the hotspots in the medical mask. The findings of this study will be of interest to policymakers, global mask manufacturers, and users, allowing them to make more informed decisions about the medical mask industry.

Emerging of composition variations of SARS-CoV-2 spike protein and human ACE2 contribute to the level of infection: in silico approaches

SARS-CoV-2 is causative of pandemic COVID-19. There is a sequence similarity between SARS-CoV-2 and SARS-CoV; however, SARS-CoV-2 RBDs (receptor-binding domain) binds 20-fold strongly with human angiotensin-converting enzyme 2 (hACE2) than SARS-CoV. The study aims to investigate protein-protein interactions (PPI) of hACE2 with SARS-CoV-2 RBD between wild and variants to detect the most influential interaction. Variants of hACE2 were retrieved from NCBI and subjected to determine the most pathogenic nsSNPs. Probability of PPIs determines the binding affinity of hACE2 genetic variants with RBD was investigated. Composition variations at the hACE2 and RBD were processed for PatchDock and refined by FireDock for the PPIs. Twelve nsSNPs were identified as the top pathogenic from SNPs (n = 7489) in hACE2 using eight bioinformatics tools. Eight RBD variants were complexed with 12 nSNPS of hACE2, and the global energy scores (Kcal/mol) were calculated and classified as very weak (-3.93 to -18.43), weak (-18.42 to -32.94), moderate (-32.94 to -47.44), strong (-47.44 to -61.95) and very strong (-61.95 to -76.46) zones. Seven composition variants in the very strong zone [G726R-G476S; R768W-V367F; Y252N-V483A; Y252N-V367F; G726R-V367F; N720D-V367F and N720D-F486L], and three in very weak [P263S-S383C; RBD-H378R; G726R-A348T] are significantly (p < 0.00001) varied for global energy score. Zonation of the five zones was established based on the scores to differentiate the effect of hACE2 and RBD variants on the binding affinity. Moreover, our findings support that the combination of hACE2 and RBD is key players for the risk of infection that should be done by further laboratory studies.Communicated by Ramaswamy H. Sarma.

Utility of P-SEP, sTREM-1 and suPAR as Novel Sepsis Biomarkers in SARS-CoV-2 Infection

The coronavirus disease 2019 is a highly contagious viral infection caused by SARS-CoV-2 virus, member of coronaviridae family. It causes life threatening complications due to complexity and rapid onset course of the disease. Early identification of high-risk patients who require close monitoring and aggressive treatment remains challengeable till date. Novel biomarkers which help to identify high risk patients at the early stage is high priority. Objective of this review to find utility of P-SEP, sTREM-1 and suPAR for diagnosis, risk stratification and prognosis of SARS-CoV-2 infected cases. Soluble receptors like, P-SEP, sTREM-1 and suPAR have been involved in immune regulation in SARS-CoV-2 infection and elevate more in severe cases. A comprehensive research of databases like PubMed, EMBASE, CNKI and Web of Science was performed for relevant studies. A total of nine out of fifteen research literature in initial screening were included for this review. Interestingly all studies have reported high levels of P-SEP, sTREM-1 and suPAR in SARS-CoV-2 infected cases and the biomarkers positively correlated with severity of infection. This implies that P-SEP, sTREM-1 and suPAR can be implemented as surrogate marker in blood profile for early diagnosis, risk stratification and prognosis in SARS-CoV-2 for better management in Indian population at the current situation.

Intestinal viral infections of nSARS-CoV2 in the Indian community: Risk of virus spread in India

In December 2019, novel severe acute respiratory syndrome coronavirus 2 (nSARS-CoV-2) virus outbreaks emerged from Wuhan, China, and spread all over the world, including India. Molecular diagnosis of Coronavirus Disease 2019 (COVID) 19 for densely and highly populated countries like India is time-consuming. A few reports have described the successful diagnosis of nSARS-CoV-2 virus from sewage and wastewater samples contaminated with fecal matter, suggesting the diagnosis of COVID 19 from the same to raise an alarm about the community transmission of virus for implementation of evacuation and lockdown strategies. So far, the association between the detection of virus and its concentration in stool samples with severity of the disease and the presence or absence of gastrointestinal symptoms have been rarely reported. We led the search utilizing multiple databases, specifically PubMed (Medline), EMBASE, and Google Scholar. We conducted a literature survey on gastrointestinal infection and the spread of this virus through fecal-oral transmission. Reports suggested that the existence and persistence of nSARS-CoV-2 in anal/rectal swabs and stool specimens for a longer period of time than in nasopharyngeal swabs provides a strong tenable outcome of gastrointestinal contamination and dissemination of this infection via potential fecal-oral transmission. This review may be helpful to conduct further studies to address the enteric involvement and excretion of nSARS-CoV-2 RNA in feces and control the community spread in both COVID-19 patients ahead of the onset of symptoms and in asymptomatic individuals through wastewater and sewage surveillance as an early indication of infection. The existence of the viral genome and active viral particle actively participate in genomic variations. Hence, we comprehended the enteric spread of different viruses amongst communities with special reference to nSARS-CoV-2.