The Novel Coronavirus: A Bird's Eye View

A closer look at the link between cycle threshold, clinical features and biomarkers: An observational study in COVID-19 patients

Background

Symptoms for severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) appear 2-3 days after exposure to the virus. Being a virus, detection is primarily by polymerase chain reaction as this offers superior sensitivity and specificity. There was a misconception that patients with low cycle threshold (Ct) have severe coronavirus disease (COVID), and for individuals with higher Ct, it is the other way around. The prognosis for COVID was derived from various biomarkers and physicians heavily relied on them.

Materials and Methods

A cross-sectional study spanning a duration of 2 years was conducted at a tertiary care centre in western India. A total of 201 individuals were included and the correlation between Ct, clinical features and biomarkers was studied.

Results

In the E-gene, 43.28% had lower Ct values and 40.79% had low Ct values in the RdRp gene. 50% of all patients had diabetes, with 60% being between the ages of 61 and 80. 54.1% of hypertension patients belonged to ages between 61 and 80. 90.54% of COVID-positive individuals had lactose dehydrogenase levels ranging from 440 to 760. 79% of patients had a procalcitonin value of more than one but less than six. 79.1% of patients had an erythrocyte sedimentation rate between 36 and 90.

Conclusion

Ct value though has a research value; it is a poor prognostic marker when compared to the various biomarkers that have been studied earlier. We cannot conclusively state that all our findings are accurate due to a lack of data but further research into the prognostic value of Ct should be conducted which will help in the ongoing scenario.

Meaning and lived experience of Iranian COVID-19 survivors: A phenomenological study

BACKGROUND

The Coronavirus (COVID-19) is among the most contagious diseases worldwide. During the first peak of the illness, COVID-19 was considered a considerable crisis for survivors. This qualitative study explored the meaning and lived experience of Iranian COVID-19 survivors. This qualitative study was conducted in Iran sometime after the onset of the coronavirus in 2020.

METHODS

This interpretative phenomenological analysis (IPA) was performed on twenty survivors of COVID-19 disease, recruited through the purposeful sampling method via in-depth semistructured interviews. The interviews were recorded and transcribed, and several codes were extracted. Data were analyzed using the MAXQDA software (v. 12).

RESULTS

The main themes and subthemes obtained from the data analysis included (1) Taboo and stigma: COVID-19 as a monster, feelings of social exclusion and loneliness, an obvious sign of shamelessness and maltreatment, (2) God's predestination: God's will and test, COVID-19 as a wake-up call to remind low human power, (3) Shadow of death: The fear of death after positive test results, death is closer than the jugular vein, the mourning of a loved one's death, and mourning for an untimely death, (4) Caregivers as an angel: Family as an unrepentant supportive, know the level of family love and attention, and (5) Rebirth and new life: understand the higher value of health and pay more attention to self-care behavior, and God gives us a golden chance to experience a better life.

CONCLUSIONS

According to the results of this study, COVID-19 survivors experience various issues regarding the nature of the disease, coping with the illness, and their social and psychological status affected by COVID-19. Considering the multidimensional supportive programs, increasing public awareness and changing negative attitudes toward the patients and survivors of the pandemic for better rehabilitation and adjustment is essential.

A Meta Modeling-Based Interoperability and Integration Testing Platform for IoT Systems

The rapid growth of the Internet of Things (IoT) and its integration into various industries has made it extremely challenging to guarantee IoT systems' dependability and quality, including scalability, dynamicity, and integration with existing IoT frameworks. However, the essential principles, approaches, and advantages of model-driven IoT testing indicate a promising strategy for overcoming these. This paper proposes a metamodeling-based interoperability and integration testing approach for IoT systems that automates the creation of test cases and the assessment of system performance by utilizing formal models to reflect the behavior and interactions of IoT systems. The proposed model-based testing enables the systematic verification and validation of complex IoT systems by capturing the essential characteristics of IoT devices, networks, and interactions. This study describes the key elements of model-driven IoT testing, including the development of formal models, methods for generating test cases, and the execution and assessment of models. In addition, it examines various modeling formalisms and their use in IoT testing, including state-based, event-driven, and hybrid models. This study examines several methods for creating test cases to ensure thorough and effective testing, such as constraint-based strategies and model coverage requirements. Model-driven IoT testing improves defect detection, expands test coverage, decreases testing effort, and increases system reliability. It also offers an organized and automated method to confirm the efficiency and dependability of IoT systems.

Impact of vaccination and non-pharmacological interventions on COVID-19: a review of simulation modeling studies in Asia

Introduction

Epidemiological modeling is widely used to offer insights into the COVID-19 pandemic situation in Asia. We reviewed published computational (mathematical/simulation) models conducted in Asia that assessed impacts of pharmacological and non-pharmacological interventions against COVID-19 and their implications for vaccination strategy.

Methods

A search of the PubMed database for peer-reviewed, published, and accessible articles in English was performed up to November 2022 to capture studies in Asian populations based on computational modeling of outcomes in the COVID-19 pandemic. Extracted data included model type (mechanistic compartmental/agent-based, statistical, both), intervention type (pharmacological, non-pharmacological), and procedures for parameterizing age. Findings are summarized with descriptive statistics and discussed in terms of the evolving COVID-19 situation.

Results

The literature search identified 378 results, of which 59 met criteria for data extraction. China, Japan, and South Korea accounted for approximately half of studies, with fewer from South and South-East Asia. Mechanistic models were most common, either compartmental (61.0%), agent-based (1.7%), or combination (18.6%) models. Statistical modeling was applied less frequently (11.9%). Pharmacological interventions were examined in 59.3% of studies, and most considered vaccination, except one study of an antiviral treatment. Non-pharmacological interventions were also considered in 84.7% of studies. Infection, hospitalization, and mortality were outcomes in 91.5%, 30.5%, and 30.5% of studies, respectively. Approximately a third of studies accounted for age, including 10 that also examined mortality. Four of these studies emphasized benefits in terms of mortality from prioritizing older adults for vaccination under conditions of a limited supply; however, one study noted potential benefits to infection rates from early vaccination of younger adults. Few studies (5.1%) considered the impact of vaccination among children.

Conclusion

Early in the COVID-19 pandemic, non-pharmacological interventions helped to mitigate the health burden of COVID-19; however, modeling indicates that high population coverage of effective vaccines will complement and reduce reliance on such interventions. Thus, increasing and maintaining immunity levels in populations through regular booster shots, particularly among at-risk and vulnerable groups, including older adults, might help to protect public health. Future modeling efforts should consider new vaccines and alternative therapies alongside an evolving virus in populations with varied vaccination histories.

Interactions between carbon nanotubes and external structures of SARS-CoV-2 using molecular docking and molecular dynamics

Molecular modeling techniques are used to describe the process of interaction between nanotubes and the main structures of the Covid-19 virus: the envelope protein, the main protease, and the Spike glycoprotein. Molecular docking studies show that the ligands have interaction characteristics capable of adsorbing the structures. Molecular dynamics simulations provide information on the mean squared deviation of atomic positions ​​between 0.5 and 3.0 Å. The Gibbs free energy model and solvent accessible surface area approaches are used. Through the results obtained through molecular dynamics simulations, it is noted that the zig-zag nanotube prefers to interact with E-pro, M-pro, and S-gly, respectively. Molecular couplings and free energy showed that the S-gly active site residues strongly interact with zigzag, chiral, and armchair nanotubes, in this order. The interactions demonstrated in this manuscript may predict some promising candidates for virus antagonists, which may be confirmed through experimental approaches.

[Risks, contamination and prevention against COVID-19 in dental work: a review]

INTRODUCTION

In April 2020 The COVID-19 pandemic caused more than one million infections and 54 600 deaths to date around the world. The spread of SARS-CoV-2 is rapid, and its transmission is through droplets of saliva, hence its importance in dentistry.

OBJECTIVE

Identify the main risks, transmission routes and prevention measures against COVID-19.

METHODS

A review of the scientific literature of the last two years on the subject was carried out in the PubMed, ScienceDirect, Google Scholar and Research Gate databases. The descriptors used were: "coronavirus", "COVID-19", "dental", "dentistry", "oral", "stomatology", and "aerosol". 350 articles were found, but 50 were selected for their topicality, relationship, and focus. The transmission of the COVID-19 is carried out mainly through saliva drops, aerosols and fomites. The virus can subsist for a time on the environment and surfaces. Dentists are health workers who are at risk of contagion because several of their procedures release aerosols. The biosecurity in the exercise of this profession must be strict and extreme, also the cleaning and disinfection of the environment and contact surfaces.

CONCLUSIONS

In the dental profession the potential risk of contamination among operators, assistants and patients is high. Knowing the causative agent and the disease allows you to reduce the possibility of contagion. The dentist must consider patients as suspects to COVID-19 and apply biosecurity at all levels.

SARS-CoV-2 and its new variants: a comprehensive review on nanotechnological application insights into potential approaches

SARS-CoV-2 (COVID-19) spreads and develops quickly worldwide as a new global crisis which has left deep socio-economic damage and massive human mortality. This virus accounts for the ongoing outbreak and forces an urgent need to improve antiviral therapeutics and targeted diagnosing tools. Researchers have been working to find a new drug to combat the virus since the outbreak started in late 2019, but there are currently no successful drugs to control the SARS-CoV-2, which makes the situation riskier. Very recently, new variant of SARS-CoV-2 is identified in many countries which make the situation very critical. No successful treatment has yet been shown although enormous international commitment to combat this pandemic and the start of different clinical trials. Nanomedicine has outstanding potential to solve several specific health issues, like viruses, which are regarded a significant medical issue. In this review, we presented an up-to-date drug design strategy against SARS-CoV-2, including the development of novel drugs and repurposed product potentials were useful, and successful drugs discovery is a constant requirement. The use of nanomaterials in treatment against SARS-CoV-2 and their use as carriers for the transport of the most frequently used antiviral therapeutics are discussed systematically here. We also addressed the possibilities of practical applications of nanoparticles to give the status of COVID-19 antiviral systems.

Covid-19 and its relation to the human eye: transmission, infection, and ocular manifestations

BACKGROUND

The world is suffering from a new strain of the coronavirus family-Covid-19. This virus strain affected different organs in the human body with a wide range of mild symptoms and moderate signs to severe and deadly ones. Multiple organs can be infected, and one of these organs is the eye. The eye is a vital organ that consists of vascular tissues and is connected to the respiratory tract through the tears and the nasolacrimal duct.

METHODS

Recent papers and research from PubMed, Researchgate, and Google Scholar were cited and thoroughly discussed. These papers were chosen based on their relevancy, reliability, publication year, published journal, and ease of accessibility to the paper itself.

RESULTS

The theory concluded that the ocular surface might consider a pathway for the virus attack and infection causation through the tears and the angiotensin-converting enzyme 2 located in the eye. This article thoroughly reviewed the history, the existing aspects of Covid-19, the ocular system features, and the claims about the possible involvement of the eye in the virus transmission along with the eye infection. There was no consensus on the eye's involvement theory.

CONCLUSION

The authors highlighted the extra work and research needed to be conducted to prove or deny these claims to provide a better understanding of the immune response of the eye to Covid-19 infection.

A comprehensive review on pharmacologic agents, immunotherapies and supportive therapeutics for COVID-19

The emergence of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has affected many countries throughout the world. As urgency is a necessity, most efforts have focused on identifying small molecule drugs that can be repurposed for use as anti-SARS-CoV-2 agents. Although several drug candidates have been identified using in silico method and in vitro studies, most of these drugs require the support of in vivo data before they can be considered for clinical trials. Several drugs are considered promising therapeutic agents for COVID-19. In addition to the direct-acting antiviral drugs, supportive therapies including traditional Chinese medicine, immunotherapies, immunomodulators, and nutritional therapy could contribute a major role in treating COVID-19 patients. Some of these drugs have already been included in the treatment guidelines, recommendations, and standard operating procedures. In this article, we comprehensively review the approved and potential therapeutic drugs, immune cells-based therapies, immunomodulatory agents/drugs, herbs and plant metabolites, nutritional and dietary for COVID-19.

COVID-19 Candidate Genes and Pathways Potentially Share the Association with Lung Cancer

COVID-19 is considered as the most challenging in the current situation but lung cancer is also the leading cause of death in the global population. These two malignancies are among the leading human diseases and are highly complex in terms of diagnostic and therapeutic approaches as well as the most frequent and highly complex and heterogeneous in nature. Based on the latest update, it is known that the patients suffering from lung cancer, are considered to be significantly at higher risk of COVID-19 infection in terms of survival and there are a number of evidences which support the hypothesis that these diseases may share the same functions and functional components. Multi-level unwanted alterations such as (epi-)genetic alterations, changes at the transcriptional level, and altered signaling pathways (receptor, cytoplasmic, and nuclear level) are the major sources which promote a number of complex diseases and such heterogeneous level of complexities are considered as the major barrier in the development of therapeutics. With so many challenges, it is critical to understand the relationships and the common shared aberrations between them which is difficult to unravel and understand. A simple approach has been applied for this study where differential gene expression analysis, pathway enrichment, and network level understanding are carried out. Since, gene expression changes and genomic alterations are related to the COVID-19 and lung cancer but their pattern varies significantly. Based on the recent studies, it appears that the patients suffering from lung cancer and and simultaneously infected with COVID-19, then survival chance is lessened. So, we have designed our goal to understand the genes commonly overexpressed and commonly enriched pathways in case of COVID-19 and lung cancer. For this purpose, we have presented the summarized review of the previous works where the pathogenesis of lung cancer and COVID-19 infection have been focused and we have also presented the new finding of our analysis. So, this work not only presents the review work but also the research work. This review and research study leads to the conclusion that growth promoting pathways (EGFR, Ras, and PI3K), growth inhibitory pathways (p53 and STK11), apoptotic pathways (Bcl- 2/Bax/Fas), and DDR pathways and genes are commonly and dominantly altered in both the cases COVID-19 and lung cancer.

Role of Potential COVID-19 Immune System Associated Genes and the Potential Pathways Linkage with Type-2 Diabetes

BACKGROUND

Coronavirus is an enclosed positive-sense RNA virus with club-like spikes extending from its surface. It is most typically associated with acute respiratory infections in humans, but its capacity to infect many host species and cause multiple illnesses makes it a complicated pathogen. The frequent encounters between wild animals and humans are a typical cause of infection. The zoonotic infections SARS-CoV and MERS-CoV are among the most common causes of serious respiratory illnesses in humans.

AIM

The main goal of this research was to look at gene expression profiles in human samples that were either infected with coronavirus or were not, and compare the varied expression patterns and their functional implications.

METHODS

The previously researched samples were acquired from a public database for this purpose, and the study was conducted, which included gene expression analysis, pathway analysis, and network-level comprehension. The results for differentially expressed genes, enriched pathways, and networks for prospective genes and gene sets are presented in the analysis. In terms of COVID-19 gene expression and its relationship to type 2 diabetes.

RESULTS

We see a lot of genes that have different gene expression patterns than normal for coronavirus infection, but in terms of pathways, it appears that there are only a few sets of functions that are affected by altered gene expression, and they are related to infection, inflammation, and the immune system.

CONCLUSION

Based on our study, we conclude that the potential genes which are affected due to infection are NFKBIA, MYC, FOXO3, BIRC3, ICAM1, IL8, CXCL1/2/5, GADD45A, RELB, SGK1, AREG, BBC3, DDIT3/4, EGR1, MTHFD2, and SESN2 and the functional changes are mainly associated with these pathways: TNF, cytokine, NF-kB, TLR, TCR, BCR, Foxo, and TGF signaling pathways are among them and there are additional pathways such as hippo signaling, apoptosis, estrogen signaling, regulating pluropotency of stem cells, ErbB, Wnt, p53, cAMP, MAPK, PI3K-AKT, oxidative phosphorylation, protein processing in endoplasmic reticulum, prolactin signaling, adipocytokine, neurotrophine signaling, and longevity regulating pathways. SMARCD3, PARL, GLIPR1, STAT2, PMAIP1, GP1BA, and TOX genes and PI3K-Akt, focal adhesion, Foxo, phagosome, adrenergic, osteoclast differentiation, platelet activation, insulin, cytokine- cytokine interaction, apoptosis, ECM, JAK-STAT, and oxytocin signaling appear as the linkage between COVID-19 and Type-2 diabetes.

Numerical study of a nonlinear COVID-19 pandemic model by finite difference and meshless methods

In this paper, a mathematical epidemiological model in the form of reaction diffusion is proposed for the transmission of the novel coronavirus (COVID-19). The next-generation method is utilized for calculating the threshold number R0 while the least square curve fitting approach is used for estimating the parameter values. The mathematical epidemiological model without and with diffusion is simulated through the operator splitting approach based on finite difference and meshless methods. Further, for the graphical solution of the non-linear model, we have applied a one-step explicit meshless procedure. We study the numerical simulation of the proposed model under the effects of diffusion. The stability analysis of the endemic equilibrium point is investigated. The obtained numerical results are compared mutually since the exact solutions are not available.

Tomographic findings and mortality in patients with severe and critical pneumonia with COVID-19 diagnosis

Introduction

A high percentage of patients with non-severe (17.9%) and severe (2.9%) atypical pneumonia do not display pulmonary tomographic findings upon hospital admission; furthermore, lesion associated with COVI-19 are peripherally distributed in a multifocal ground-glass pattern, as well as displaying an irregular consolidation pattern, with a posterior or lower lobe predilection. The main objective of this study was to identify the pulmonary radiological patterns in patients diagnosed with SARS-CoV-2 pneumonia, the factors associated with the need for mechanical ventilation, as well as their survival rates at 30 days.

Methods

We report the pulmonary tomographic findings of 490 consecutive patients with severe and critical pneumonia due to SARS-CoV-2. The patients were classified according to the tomography and demographic findings, sepsis severity prognostic scales, Charlson comorbidity index (CCI), the Sequential Organ Failure Assessment (SOFA), and the Acute Physiology and Chronic Health Evaluation (APACHE IV). The Kaplan-Meier method was used to calculate survival distributions.

Results

89.80% of patients had ground-glass opacities, 81.63% radiologic consolidation sign, 42.45% vascular thickening pattern, 37.55% lymphadenopathies, 14.90% pleural effusion, and 2.65% pulmonary thrombosis; meanwhile, 91.02% had bilateral lesions, 85.51% had peripheral lesions, and 75.92% had basal lobe lesions. APACHE IV (HR, 1.191, 95% CI [1.126, 1.260]), SOFA (HR, 5.178, 95%CI [3.103, 8.641]), and CCI (HR, 0.673, 95%CI [0.510, 0.889]), as well as the pulmonary damage severity index (HR, 1.282, 95%CI [1.151, 1.428]), predict the need for invasive mechanical ventilation. Only moderate ARDS patients with mild and severe lung disease showed different 30-day mortality distributions (χ² = 7.00, p = 0.008).

Discussion

Although the survival distributions did not vary significantly, an overwhelming majority of patients (i.e., 84.35%) with a higher pulmonary damage severity index (i.e., 23>) died within 30 days of hospital admission, while only 25.91% with moderate lung damage and 2.42% with mild lung damage.

Comprehensive analysis of pathways in Coronavirus 2019 (COVID-19) using an unsupervised machine learning method

The World Health Organization (WHO) introduced “Coronavirus disease 19” or “COVID-19” as a novel coronavirus in March 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires the fast discovery of effective treatments to fight this worldwide crisis. Artificial intelligence and bioinformatics analysis pipelines can assist with finding biomarkers, explanations, and cures. Artificial intelligence and machine learning methods provide powerful infrastructures for interpreting and understanding the available data. On the other hand, pathway enrichment analysis, as a dominant tool, could help researchers discover potential key targets present in biological pathways of host cells that are targeted by SARS-CoV-2. In this work, we propose a two-stage machine learning approach for pathway analysis. During the first stage, four informative gene sets that can represent important COVID-19 related pathways are selected. These “representative genes” are associated with the COVID-19 pathology. Then, two distinctive networks were constructed for COVID-19 related signaling and disease pathways. In the second stage, the pathways of each network are ranked with respect to some unsupervised scorning method based on our defined informative features. Finally, we present a comprehensive analysis of the top important pathways in both networks. Materials and implementations are available at: https://github.com/MahnazHabibi/Pathway.

Jordanian Nurses’ Knowledge, Attitudes, and Willingness to Provide Care to Patients with COVID-19

Background:

previous studies showed that nurses reported inadequate knowledge of the risks and protective strategies in dealing with infectious diseases. Additionally, nurses reported a lack of willingness to care for patients with infectious diseases.

Purpose:

To examine Jordanian nurses’ knowledge and attitudes and their willingness to provide care for patients with COVID-19.

Design and Methods:

Correlational cross-sectional design with convenience sampling was used to collect data through an online self-administered questionnaire from 347 Jordanian nurses working at hospitals.

Results:

The study results showed that about 56% of the nurses reported having the experience of treating or providing care to confirmed or suspected COVID-19 patients, and 71.8% expressed their willingness to provide care for them. Only 55% of the nurses reported finishing a training program about COVID-19. Job title, type of hospital, and experience in treating or caring for patients with COVID-19 were predictors of nurses’ willingness to provide care.

Conclusion:

Jordanian nurses reported gaps in their knowledge about COVID-19 related to using personal protective equipment and fear of transmitting the disease to family members. Nurses also reported a moderate level of attitude toward hand hygiene and the use of personal protective equipment; however, most of the nurses reported willingness to provide care for COVID-19 patients.

An intelligent forecast for COVID‐19 based on single and multiple features

It is urgent to identify the development of the Corona Virus Disease 2019 (COVID‐19) in countries around the world. Therefore, visualization is particularly important for monitoring the COVID‐19. In this paper, we visually analyze the real‐time data of COVID‐19, to monitor the trend of COVID‐19 in the form of charts. At present, the COVID‐19 is still spreading. However, in the existing works, the visualization of COVID‐19 data has not established a certain connection between the forecast of the epidemic data and the forecast of the epidemic. To better predict the development trend of the COVID‐19, we establish a logistic growth model to predict the development of the epidemic by using the same data source in the visualization. However, the logistic growth model only has a single feature. To predict the epidemic situation in an all‐round way, we also predict the development trend of the COVID‐19 based on the Susceptible Exposed Infected Removed epidemic model with multiple features. We fit the data predicted by the model to the real COVID‐19 epidemic data. The simulation results show that the predicted epidemic development trend is consistent with the actual epidemic development trend, and our model performs well in predicting the trend of COVID‐19.

The Impact of Changes regarding Working Circumstances during COVID-19 Pandemic upon Patients Evaluated for Thyroid Dysfunction

We evaluated patients who presented with thyroid dysfunction correlated symptoms that started when the Government took important measures to reduce the spread of COVID-19. These measures have influenced the safety of many people’s jobs. Data were collected from 378 patients that were clinically evaluated at the Endocrinology Department, between September 2020 and January 2021. Their health status modifications were statistically analyzed in correlation with their life and work changes. These changes were induced by measures associated with the COVID-19 pandemic. The lifestyle changes correlated with the COVID-19 pandemic have been present in both categories of patients: euthyroid and dysthyroid patients; 87.50% of euthyroid patients physically felt the pandemic-induced changes in their lives. It resulted in changes in lifestyle and job insecurity has a statistically significant influence (p < 0.01) on their state of health. The presence of life/work changes in men is strongly reflected in their state of health (p = 0.0004). Work instability that occurred as a side effect of the COVID-19 pandemic induced symptoms that made many people believe they have an endocrinology disorder.

A survey on the correlation between PM2.5 concentration and the incidence of suspected and positive cases of COVID-19 referred to medical centers: A case study of Tehran

COVID-19, one of the greatest health challenges of the present century, has infected millions of people and caused more than 6 million deaths worldwide. The causative agent of this disease is the new virus SARS-CoV-2; which continues to spread globally and sometimes with new and more complex aspects than before. The present study is an observational study aimed to investigate the role of AQI; PM_2.5 and its relationship with the incidence of suspected cases (SC) and positive cases (PC) of COVID-19 at different levels of the air quality index (AQI) in Tehran, the capital of Iran in the period from Feb 20th, 2020 to Feb 22nd, 2021. Data on AQI were collected online from the air monitoring website of Air Quality Control Company under the supervision of Tehran Municipality. The data on suspected and positive cases were obtained from the Iranian Ministry of Health. The results and statistical analysis (Pearson correlation test) showed that with the increase of AQI level, the number of suspected cases (SC) and positive cases (PC), also increased (P-value<0.01). The average daily number of suspected and positive COVID-19 cases referred to medical centers, at different levels of the AQI was as follows: level II: yellow, moderate (SC: N_ave = 466; PC: N_ave = 223), level III: orange, unhealthy for sensitive groups (SC: N_ave = 564; PC: N_ave = 275), and Level IV: red, unhealthy (SC: N_ave = 558; PC: N_ave = 294). The results of the GEE for seasonal comparison (winter as reference season), showed that there is an epidemiological pattern in autumn with colder weather compared to other seasons in both suspected (Cl: %95, B = 408.94) and positive (Cl: %95, B = 83.42) cases of COVID-19. The results of this study will serve policymakers as an informative tool for guidance on the importance of the role of air pollution in viral epidemics.

In COVID-19 Patients, the Identified Gastrointestinal Symptoms in Tertiary Care Center of India

Aim

Materials and methods

Results

Conclusion

How to cite this article

Antibody Response to COVID-19 mRNA Vaccines in Oncologic and Hematologic Patients Undergoing Chemotherapy

BACKGROUND

Information on immune responses in cancer patients following mRNA COVID-19 vaccines is still insufficient, but generally, patients had impaired serological responses, especially those with hematological malignancies. We evaluated serological response to COVID-19 mRNA vaccine in cancer patients receiving chemotherapy compared with healthy controls.

METHODS

In total, 195 cancer patients and 400 randomly selected controls who had been administered a Pfizer-BioNTech or Moderna COVID-19 vaccines in two doses were compared. The threshold of positivity was 4.33 BAU/mL. Patients were receiving anticancer treatment after the first and second dose of the vaccines.

RESULTS

a TOTAL OF 169 patients (87%) had solid tumors and 26 hemolymphopoietic diseases. Seropositivity rate was lower in patients than controls (91% vs. 96%), with an age/gender-adjusted rate ratio (RR) of 0.95 (95% CL = 0.89-1.02). Positivity was found in 97% of solid cancers and in 50% of hemolymphopoietic tumors. Both advanced and adjuvant therapy seemed to slightly reduce seropositivity rates in patients when compared to controls (RR = 0.97, 95% CL = 0.89-1.06; RR = 0.94, 95% CL = 0.87-1.01).

CONCLUSIONS

the response to vaccination is similar in patients affected by solid tumors to controls. On the contrary, hemolymphopietic patients show a much lower response than controls.

Post-Covid-19 Rhino-Cerebral Mucormycosis: an Observational Study During the Second Wave

Mucormycosis is one of the most lethal and rapidly spreading fungal infection which is caused by fungus of the order Mucorales. The swiftness of spreading and high mortality rate that characterize mucormycosis cases added more burden to the enormous challenge brought by the Covid-19 pandemic globally. The aim of this article is to identify and discuss mucormycosis and review the literature related to its diagnosis and management. A total of 15 mucormycosis cases with a history of Covid-19 infection were identified in the Department of Dentistry of Shri B M Patil Medical College Hospital and Research Centre BLDE (Deemed to be University), Vijayapura, India. The duration of the study was between April 1st and mid-September 2021. Nasal swab and tissue samples from oral and maxillofacial region were collected. Blood investigations, RT-PCR and HbA1c tests and radiography revealed changes in the trabecular pattern and bone loss associated with periodontal inflammation. Mucormycosis is a life-threatening infection. Hence, dental and other clinical professionals must be aware of this possible fatal complication, so as to avoid an unfavorable outcome in clinical practice.

Modeling the dynamics of COVID-19 using fractal-fractional operator with a case study

This research study consists of a newly proposed Atangana-Baleanu derivative for transmission dynamics of the coronavirus (COVID-19) epidemic. Taking the advantage of non-local Atangana-Baleanu fractional-derivative approach, the dynamics of the well-known COVID-19 have been examined and analyzed with the induction of various infection phases and multiple routes of transmissions. For this purpose, an attempt is made to present a novel approach that initially formulates the proposed model using classical integer-order differential equations, followed by application of the fractal fractional derivative for obtaining the fractional COVID-19 model having arbitrary order Ψ and the fractal dimension Ξ . With this motive, some basic properties of the model that include equilibria and reproduction number are presented as well. Then, the stability of the equilibrium points is examined. Furthermore, a novel numerical method is introduced based on Adams-Bashforth fractal-fractional approach for the derivation of an iterative scheme of the fractal-fractional ABC model. This in turns, has helped us to obtained detailed graphical representation for several values of fractional and fractal orders Ψ and Ξ , respectively. In the end, graphical results and numerical simulation are presented for comprehending the impacts of the different model parameters and fractional order on the disease dynamics and the control. The outcomes of this research would provide strong theoretical insights for understanding mechanism of the infectious diseases and help the worldwide practitioners in adopting controlling strategies.

Clinical analysis of severe COVID-19 patients

BACKGROUND:

Patients with unexplained pneumonia appeared in Wuhan, Hubei Province at the end of 2019.

OBJECTIVE:

To analyze the clinical data of patients with severe COVID-19.

METHODS:

Medical records of 28 severe patients admitted to the intensive care unit of Wuhan Xinzhou District People’s Hospital were collected from January 31 to March 17.

RESULTS:

The mortality rate of severe patients in our study was 39.3%. There were statistically significant differences in age, admission systolic blood pressure, lymphocyte count, albumin, total bilirubin, and lactate dehydrogenase between the death group and the survival group (P< 0.05). There were statistically significant differences in APACHE II, CURB-65, SOFA, respiratory frequency, systolic pressure, platelet, procalcitonin, albumin, creatinine, creatine kinase isoenzyme, lactate dehydrogenase, chloride ion, prothrombin time, international normalized ratio, arterial partial pressure of oxygen, and FiO2 at ICU between the death group and the survival group (P< 0.05).

CONCLUSIONS:

Fever and cough are the main symptoms, which is useful for predicting the prognosis to dynamically measure the APACHE II, CURB-65, SOFA, respiratory frequency, lymphocyte count, platelet, lactate dehydrogenase, and coagulation tests. The drugs that protect the liver and heart may improve the survival rate of patients with severe COVID-19.

Neutralizing antibody: a savior in the Covid-19 disease

Coronavirus outbreak was declared a pandemic by World Health Organization (WHO) in March 2020. The pandemic has led to a devastating loss of life. It has shown us how infectious diseases can cause human existence at stake, and community health is important. The spike protein is the most immunogenic component of the virus. Most vaccine development strategies have focused on the receptor-binding domain (RBD) in the spike protein because it is the most specific target site that recognizes and interacts with human lung cells. Neutralizing antibodies are generated by the humoral immune system and reduce the viral load by binding to spike protein components. Neutralizing antibodies are the proteins secreted by plasma cells and serve as an important part of the defense mechanism. In the recent Covid-19 infection, neutralizing antibodies can be utilized for both diagnostic such as immune surveillance and therapeutic tools such as plasma therapy. So far, many monoclonal antibodies are in the clinical trial phase, and few of them are already in use. In this review, we have discussed details about neutralizing antibodies and their role in combating Covid-19 disease.

Total synthesis of remdesivir

Remdesivir, the first drug approved by the FDA to treat COVID-19, is in high demand for patients infected with the SARS-CoV-2 virus. Herein, we report a facile approach minimizing the protecting group manipulations to afford remdesivir in good overall yield.

Perceived fear of COVID-19 infection according to sex, age and occupational risk using the Brazilian version of the Fear of COVID-19 Scale

We investigated the fear of COVID-19 infection after proper translation and cultural adaptation of the "Fear of COVID-19 Scale" to the Brazilian Portuguese language. A sample of 1,743 Brazilian participants were included. The scale showed excellent psychometric characteristics. Women showed higher anxiety levels. Fear of COVID-19 scores were lower in males with occupational risk of contamination. On the other hand, women and younger individuals showed higher fear of COVID-19 infection scores. The Brazilian Fear of COVID-19 Scale proved to be a reliable tool with excellent psychometric properties for identifying fear of COVID-19 infection in the Brazilian population.

Impact of COVID-19 on psychological and academic performance of medical students in Saudi Arabia

Background and Objectives:

The COVID-19 pandemic affected the mental health and psychosocial conditions of everyone worldwide according to the WHO. Public health emergencies affect college students and are expressed as anxiety, worry, and fear. The aim of this study was to assess the impact of COVID-19 on the psychological health and performance of medical students.

Design and Settings:

A cross-sectional study using an online survey was done.

Participants and Methods:

Participants were 1591 Saudi medical students. A predesigned questionnaire included questions on demographic characters, GPA, having a relative got COVID-19, how to face sad news and stressors, and satisfaction with online lectures. The Generalized Anxiety Disorder (GAD-7) scale was used that included seven items asking about the degree the participant was bothered by feeling anxious in the last 2 weeks.

Results:

A total of 59.4% of students had various degrees of anxiety. Participant age, unsteady family income, high grade point average (GPA,) satisfaction with the online lectures, and being female were associated with higher GAD-7 scores.

Conclusion:

Mental health of medical students was significantly affected by the COVID-19 pandemic. Psychological support programs for medical students during the pandemic and provision of high-quality distance learning is essential for psychological well-being during the pandemic.

Virucidal effect of povidone-iodine against SARS-CoV-2 in vitro

Objective

To evaluate the antiviral activity of the oral disinfectant povidone-iodine (PVP-I) against severe acute respiratory syndrome-coronavirus-2 (SARS-CoV2) in vitro.

Methods

The cytotoxic effects of PVP-I were determined in Vero and Calu-3 cell lines using that by Cell Counting Kit-8 assay. Viral load in the cell culture medium above infected cells was quantitated using real-time polymerase chain reaction. The cytopathic effect (CPE) and viral infective rate were observed by immunofluorescence microscopy.

Results

PVP-I at a concentration >0.5 mg/ml in contact with SARS-CoV-2 for 30 s, 1 min, 2 min and 5 min showed up to 99% viral inhibition. For in vitro testing, upon exposure for 1 min, PVP-I showed a virucidal effect. PVP-I had no cytotoxic effects at the range of concentrations tested (0.125–1 mg/ml; CC₅₀ > 2.75 mM) in Vero and Calu-3 cells.

Conclusion

These results demonstrate that the ideal contact time was 1 min and the optimal concentration was 1 mg/ml, which provides an experimental basis for the use of oral disinfectants in dental hospitals.

What drives beliefs in COVID-19 conspiracy theories? The role of psychotic-like experiences and confinement-related factors

Rationale

The COVID-19 pandemic is a worldwide threat to public health and the global economy. The climate of fear and uncertainty associated with the pandemic has fostered the emergence of a wide range of COVID-19 conspiracy theories that have the potential to shape public opinion and hinder the effective dissemination of valid information. Beliefs in conspiracy theories have been associated with maladaptive personality traits such as schizotypy and paranoia, as well as other non-psychotic psychological characteristics (e.g., social isolation, stress).

Methods

An online survey was conducted to examine the associations between beliefs in COVID-19 conspiracy theories and psychotic-like experiences in a Portuguese community sample (N = 438), while also addressing the role of sociodemographic variables, psychological outcomes (e.g., stress, affective states), confinement-related factors (e.g., confinement conditions/behaviors), and pandemic-related factors (e.g., health concerns, financial issues).

Results

Findings suggest that psychotic-like experiences are associated with beliefs in COVID-19 conspiracy theories, particularly perceptual abnormalities and persecutory ideation. Moreover, increased health-related concerns and reduced education levels also seem to be liability factors for these conspiracy beliefs.

Conclusion

These results add important insights into how the adherence to illogical and erroneous disease-related arguments can be related to psychotic-like experiences. COVID-19 conspiracy theories are yet another major challenge that governments and policymakers must contemplate when defining strategic directions to manage the current and future pandemics.

Therapeutic Uses of Traditional Chinese Medicines Against COVID-19

COVID-19 is a pandemic and a serious respiratory disorder that is caused by coronavirus. It has produced an outbreak of acute infectious pneumonia in China and afterward all around the world. There is not a single anti-viral drug, vaccine or any kind of treatment available for this fatal disease. There are only a few options available for symptomatic relief. Thus, in China, 85% of SARS-CoV-2 infected individuals have been treated with traditional Chinese medicines (TCM). Thus, this article focused on the previous kinds of literature regarding COVID-19 and its treatment with TCM along with its applications. SARS-CoV-2 and SARS-CoV showed similarity in genes, pathological processes, and epidemiology, so these can be treated with TCM. The proof regarding treatment of SARS-CoV with TCM explicitly shows the advantages of using TCM therapy for COVID-19. Present literature explains the mode of action and efficacy of TCM and elaborates on the natural compounds introduced to treat COVID-19.

Systemic Inflammation and Complement Activation Parameters Predict Clinical Outcome of Severe SARS-CoV-2 Infections

Overactivation of the complement system has been characterized in severe COVID-19 cases. Complement components are known to trigger NETosis via the coagulation cascade and have also been reported in human tracheobronchial epithelial cells. In this longitudinal study, we investigated systemic and local complement activation and NETosis in COVID-19 patients that underwent mechanical ventilation. Results confirmed significantly higher baseline levels of serum C5a (24.5 ± 39.0 ng/mL) and TCC (11.03 ± 8.52 µg/mL) in patients compared to healthy controls (p < 0.01 and p < 0.0001, respectively). Furthermore, systemic NETosis was significantly augmented in patients (5.87 (±3.71) × 10⁶ neutrophils/mL) compared to healthy controls (0.82 (±0.74) × 10⁶ neutrophils/mL) (p < 0.0001). In tracheal fluid, baseline TCC levels but not C5a and NETosis, were significantly higher in patients. Kinetic studies of systemic complement activation revealed markedly higher levels of TCC and CRP in nonsurvivors compared to survivors. In contrast, kinetic studies showed decreased local NETosis in tracheal fluid but comparable local complement activation in nonsurvivors compared to survivors. Systemic TCC and NETosis were significantly correlated with inflammation and coagulation markers. We propose that a ratio comprising systemic inflammation, complement activation, and chest X-ray score could be rendered as a predictive parameter of patient outcome in severe SARS-CoV-2 infections.

Autophagy: The Potential Link between SARS-CoV-2 and Cancer

Simple Summary

Coronavirus disease 2019 (COVID-19) has led to a global crisis. With the increasing number of individuals infected worldwide, the long-term consequences of this disease have become an active area of research. The constellation of symptoms COVID-19 survivors suffer from is commonly referred to as post-acute COVID-19 syndrome in the scientific literature. In this paper, we discuss the potential long-term complications of this infection resulting from the persistence of the viral particles in body tissues interacting with host cells’ autophagy machinery in the context of the development of cancer, cancer progression and metastasis, as well as response to treatment. We also propose a structured framework for future studies to investigate the potential impact of COVID-19 infection on cancer.

Abstract

COVID-19 infection survivors suffer from a constellation of symptoms referred to as post-acute COVID-19 syndrome. However, in the wake of recent evidence highlighting the long-term persistence of SARS-CoV-2 antigens in tissues and emerging information regarding the interaction between SARS-CoV-2 proteins and various components of the host cell macroautophagy/autophagy machinery, the unforeseen long-term consequences of this infection, such as increased risk of malignancies, should be explored. Although SARS-CoV-2 is not considered an oncogenic virus, the possibility of increased risk of cancer among COVID-19 survivors cannot be ruled out. Herein, we provide an overview of the possible mechanisms leading to cancer development, particularly obesity-related cancers (e.g., colorectal cancer), resulting from defects in autophagy and the blockade of the autophagic flux, and also immune escape in COVID-19 survivors. We also highlight the potential long-term implications of COVID-19 infection in the prognosis of patients with cancer and their response to different cancer treatments. Finally, we consider future directions for further investigations on this matter.

Discovery and Nanosized Preparations of (S,R)-Tylophorine Malate as Novel anti-SARS-CoV-2 Agents

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has stimulated the search for effective drugs for its prevention and treatment. Natural products are an important source for new drug discovery. Here, we report that, NK007(S,R), a tylophorine malate, displays high antiviral activity against SARS-CoV-2 with an EC₅₀ 0.03 μM in vitro, which is substantially lower than that of remdesivir (EC₅₀: 0.8 μM in vitro), the only authorized drug to date. The histopathological research revealed that NK007(S,R) (5 mg/kg/dose) displayed a protection effect in lung injury induced by SARS-CoV-2, which is better than remdesivir (25 mg/kg/dose). We also prepared two nanosized preparations of NK007(S,R), which also showed good efficacy (EC₅₀: NP-NK007, 0.007 μM in vitro; LP-NK007, 0.014 μM in vitro). Our findings suggest that tylophora alkaloids, isolated from the traditional Chinese medicine Cynanchum komarovii AL, offer a new skeleton for the development of anticoronavirus drug candidate.

Microbiota, probiotics and respiratory infections: the three musketeers can tip off potential management of COVID-19

Rapid infectivity of SARS-CoV2 with recent viral variants is posing a challenge in the development of robust therapeutic strategies. On the other hand, microbiota is debated for its involvement in SARS-CoV2 infection with varied opinions. Although ample data about the role of microbiota and probiotics in respiratory viral infections are available, their role in COVID-19 is limited albeit emerging rapidly. The utilization of probiotics for the management of COVID-19 is still under investigation in many clinical trials. Existing information coupled with recent COVID-19 related studies can suggest various ways to use microbiota modulation and probiotics for managing this pandemic. Present article indicates the role of microbiota modulation and probiotics in respiratory infections. In addition, scattered evidence was gathered to understand the potential of microbiota and probiotics in the management of SARS-CoV2. Gut-airway microbiota connection is already apparent in respiratory tract viral infections, including SARS-CoV2. Though few clinical trials are evaluating microbiota and probiotics for COVID-19 management, the safety evaluation must be given more serious consideration because of the possibility of opportunistic infections among COVID-19 patients. Nevertheless, the information about microbiota modulation using probiotics and prebiotics can be helpful to manage this outbreak and this review presents different aspects of this idea.

In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials

Despite strict measures taken by many countries, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be an issue of global concern. Currently, there are no clinically proven pharmacotherapies for coronavirus disease 2019, despite promising initial results obtained from drugs such as azithromycin and hydroxychloroquine. Therefore, the repurposing of clinically approved drugs for use against SARS-CoV-2 has become a viable strategy. Here, we searched for drugs that target SARS-CoV-2 3C-like protease (3CLpro) and viral RNA-dependent RNA polymerase (RdRp) by in silico screening of the U.S. Food and Drug Administration approved drug library. Well-tolerated and widely used drugs were selected for molecular dynamics (MD) simulations to evaluate drug-protein interactions and their persistence under physiological conditions. Tetracycline, dihydroergotamine, ergotamine, dutasteride, nelfinavir, and paliperidone formed stable interactions with 3CLpro based on MD simulation results. Similar analysis with RdRp showed that eltrombopag, tipranavir, ergotamine, and conivaptan bound to the enzyme with high binding free energies. Docking results suggest that ergotamine, dihydroergotamine, bromocriptine, dutasteride, conivaptan, paliperidone, and tipranavir can bind to both enzymes with high affinity. As these drugs are well tolerated, cost-effective, and widely used, our study suggests that they could potentially to be used in clinical trials for the treatment of SARS-CoV-2-infected patients.Communicated by Ramaswamy H. Sarma.

Smart delivery and retrieval of swab collection kit for COVID-19 test using autonomous Unmanned Aerial Vehicles

Drones, also known as Unmanned Aerial Vehicles (UAVs), are one of the highly emerging technologies of the modern day. Due to their small size, flying capabilities, and complex machinery, drones can be deployed in diverse fields, including agriculture, sports, entertainment, parcel delivery, disaster management, search and rescue, emergency medicine, and healthcare. In case of medical emergency, timely delivery of the required emergency kit is very important. This is often not possible in many underdeveloped countries due to lack of resources, traffic jams, congestion or challenging routes. Also, in times like today’s when the world is hit with COVID-19 pandemic, the movement is very limited due to lockdowns and emergency. In such case, drones can be deployed to deliver the emergency kits and collect samples for tests. This may save someones life as well as time and financial resources. In third world countries, the COVID-19 has spread chaos because of very limited hospitals, resources and staff. Therefore, it is difficult for the government and health officials to accommodate every patient or give him/her the care that he/she needs. Amidst the fear of pandemic, everyone is trying to undergo tests for COVID-19 which is difficult to handle In our research, we have proposed a solution that comprises smartphone application with the help of a patient sending a call to a healthcare centre for delivering emergency kit. The kit contains equipment with the help of which a person can collect swab. The drone takes the swab samples back to the healthcare centre for tests. We have introduced an optimization factor as a baseline for future studies of this kind. We have further conducted field experiments to test our proposed scheme. The results have shown that drones can be quite efficient in collecting samples and delivering emergency kits.

Dissection of non-pharmaceutical interventions implemented by Iran, South Korea, and Turkey in the fight against COVID-19 pandemic

Purpose

The novel coronavirus disease 2019 (COVID-19) has imposed a great global burden on public health. As one of the most affected countries, Iran has tackled emerging challenges in the path to overcoming the epidemic, with three peaks of the disease propagation as of February 19, 2020. To flatten the curve of the COVID-19 pandemic, most countries have implemented bundles of intrusive, sometimes extremely stringent non-pharmaceutical interventions (NPIs). In this communication, we have dissected the effectiveness of NPIs and compared the strategies implemented by Iran, Turkey, and South Korea to mitigate the disease’s spread.

Methods

We searched online databases via PubMed, Web of Knowledge, and Scopus. Titles/abstracts and full-texts were screened by two reviewers and discrepancies were resolved upon discussion.

Results

Our results provide insights into five domains: prevention, screening, in-patient and out-patient facilities, governance, and management of diabetes mellitus. Analysis of previous efforts put in place illustrates that by fostering efficient social distancing measures, increasing the capability to perform prompt polymerase chain reaction tests, applying smart contact tracing, and supplying adequate personal protective equipment, Turkey and South Korea have brought the epidemic sub-optimally under control.

Conclusion

From the perspective of policymakers, these achievements are of utmost importance given that attaining the aspirational goals in the management of the COVID-19 necessities a suitable adjustment of previous successful strategies. Hence, policymakers should be noticed that a suitable combination of NPIs is necessary to stem the disease’s propagation.

SARS-CoV-2 on Ocular Surfaces in a Cohort of Patients With COVID-19 From the Lombardy Region, Italy

Importance

Since February 2020, coronavirus disease 2019 (COVID-19) has spread rapidly all over the world, with an epidemiological cluster in Lombardy, Italy. The viral communicability may be mediated by various body fluids, but insufficient information is available on the presence of the virus in human tears.

Objectives

To investigate the rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in tears collected from patients with COVID-19 by means of real-time reverse transcriptase-polymerase chain reaction (rRT-PCR) assay and to assess the association of virus presence with concomitant clinical conditions.

Design, Setting, and Participants

Cross-sectional study conducted between April 9 and May 5, 2020. The setting was intensive care units at Azienda Socio-Sanitaria Territoriale (ASST) Sette-Laghi Hospital, University of Insubria, in Varese, Lombardy, Italy. A conjunctival swab was performed in 91 patients hospitalized for COVID-19, which was clinically diagnosed by rRT-PCR assay on nasopharyngeal swabs and by radiological imaging. Conjunctival swabs from 17 additional healthy volunteer participants with no symptoms of COVID-19 were examined to evaluate the availability and applicability of the conjunctival swab test.

Exposure

SARS-CoV-2 detection by means of rRT-PCR assay performed on the collected samples obtained by conjunctival swabs.

Main Outcomes and Measures

Conjunctival swab and nasopharyngeal swab results are reported, as well as demographic and clinical data.

Results

A total of 108 participants (mean [SD] age, 58.7 [14.2] years; 55 female and 53 male) were tested for SARS-CoV-2 using rRT-PCR assay, including 91 patients hospitalized with COVID-19 and 17 were healthy volunteers. SARS-CoV-2 was found on the ocular surface in 52 of 91 patients with COVID-19 (57.1%; 95% CI, 46.3%-67.5%), with a wide variability in the mean viral load from both eyes. Among a subset of 41 patients, concordance of 63.0% (95% CI, 41.0%-81.0%) was found between positive conjunctival and nasopharyngeal swab test results when performed within 2 days of each other. In 17 of these patients, nasopharyngeal swab results were negative for SARS-CoV-2. In 10 of these 17 patients, conjunctival swab results were positive for the virus.

Conclusions and Relevance

In this study, SARS-CoV-2 RNA was found on the ocular surface in a large part of this cohort of patients with COVID-19, although the infectivity of this material could not be determined. Because patients may have positive test results with a conjunctival swab and negative results with a nasopharyngeal swab, use of the slightly invasive conjunctival swab may be considered as a supplementary diagnostic test.

Molecular diagnostic assays for COVID-19: an overview

The coronavirus disease 2019 (COVID-19) pandemic has highlighted the cardinal importance of rapid and accurate diagnostic assays. Since the early days of the outbreak, researchers with different scientific backgrounds across the globe have tried to fulfill the urgent need for such assays, with many assays having been approved and with others still undergoing clinical validation. Molecular diagnostic assays are a major group of tests used to diagnose COVID-19. Currently, the detection of SARS-CoV-2 RNA by reverse transcription polymerase chain reaction (RT-PCR) is the most widely used method. Other diagnostic molecular methods, including CRISPR-based assays, isothermal nucleic acid amplification methods, digital PCR, microarray assays, and next generation sequencing (NGS), are promising alternatives. In this review, we summarize the technical and clinical applications of the different COVID-19 molecular diagnostic assays and suggest directions for the implementation of such technologies in future infectious disease outbreaks.

Systematic Review and Meta-Analysis of Tocilizumab Therapy versus Standard of Care in over 15,000 COVID-19 Pneumonia Patients during the First Eight Months of the Pandemic

BACKGROUND

Tocilizumab is an anti-IL-6 therapy widely adopted in the management of the so-called "cytokine storm" related to SARS-CoV-2 virus infection, but its effectiveness, use in relation to concomitant corticosteroid therapy and safety were unproven despite widespread use in numerous studies, mostly open label at the start of the pandemic.

METHODS

We performed a systematic review and meta-analysis of case-control studies utilising tocilizumab in COVID-19 on different databases (PubMed/MEDLINE/Scopus) and preprint servers (medRxiv and SSRN) from inception until 20 July 2020 (PROSPERO CRD42020195690). Subgroup analyses and meta-regressions were performed. The impact of tocilizumab and concomitant corticosteroid therapy or tocilizumab alone versus standard of care (SOC) on the death rate, need for mechanical ventilation, ICU admission and bacterial infections were assessed.

RESULTS

Thirty-nine studies with 15,531 patients (3657 cases versus 11,874 controls) were identified. Unadjusted estimates (n = 28) failed to demonstrate a protective effect of tocilizumab on survival (OR 0.74 ([95%CI 0.55-1.01], p = 0.057), mechanical ventilation prevention (OR 2.21 [95%CI 0.53-9.23], p = 0.277) or prevention of ICU admission (OR 3.79 [95%CI 0.38-37.34], p = 0.254). Considering studies with adjusted, estimated, tocilizumab use was associated with mortality rate reduction (HR 0.50 ([95%CI 0.38-0.64], p < 0.001) and prevention of ICU admission (OR 0.16 ([95%CI 0.06-0.43], p < 0.001). Tocilizumab with concomitant steroid use versus SOC was protective with an OR of 0.49 ([95%CI 0.36-0.65], p < 0.05) as was tocilizumab alone versus SOC with an OR of 0.59 ([95%CI 0.34-1.00], p < 0.001). Risk of infection increased (2.36 [95%CI 1.001-5.54], p = 0.050; based on unadjusted estimates).

CONCLUSION

Despite the heterogeneity of included studies and large number of preprint articles, our findings from the first eight of the pandemic in over 15,000 COVID-19 cases suggested an incremental efficacy of tocilizumab in severe COVID-19 that were confirmed by subsequent meta-analyses of large randomized trials of tocilizumab. This suggests that analysis of case-control studies and pre-print server data in the early stages of a pandemic appeared robust for supporting incremental benefits and lack of major therapeutic toxicity of tocilizumab for severe COVID-19.

Impact of Age and Sex on Antibody Response Following the Second Dose of COVID-19 BNT162b2 mRNA Vaccine in Greek Healthcare Workers

Anti-SARS-CoV-2 spike RBD (receptor-binding domain) IgG antibody levels were monitored in 1643 volunteer healthcare workers of Eginition, Evangelismos, and Konstantopoulio General Hospitals (Athens, Greece), who underwent vaccination with two doses of COVID-19 BNT162b2 mRNA vaccine (Pfizer) and had no history of SARS-CoV-2 infection. Venous blood was collected 20–30 days after the second vaccine dose and anti-RBD IgG levels were determined using CMIA SARS-CoV-2 IgG II Quant (Abbott) on ARCHITECT i System or ADVIA Centaur SARS-CoV-2 IgG (Siemens) on Centaur XP platform. From the total population of 1643 vaccinees (533 M/1110 F; median age = 49; interquartile range-IQR = 40–56), 1636 (99.6%) had anti-SARS-CoV-2 IgG titers above the positivity threshold of the assay used. One-Way ANOVA Kruskal-Wallis H test showed a statistically significant difference in the median of antibody titers between the different age groups (p < 0.0001). Consistently, Spearman’s correlation coefficient (r) for IgGs and age as continuous variables was −0.2380 (p = 1.98 × 10⁻¹⁷). Moreover, antibody titers were slightly higher by 1.2-mean fold (p = 3 × 10⁻⁶) in the total female population of the three hospitals (median = 1594; IQR = 875–2584) as compared to males (median = 1292; IQR = 671.9–2188). The present study supports that BNT162b2 vaccine is particularly effective in producing high anti-SARS-CoV-2 IgG levels in healthy individuals, and this humoral response is age- and gender-dependent.

Effectiveness of ozone therapy in addition to conventional treatment on mortality in patients with COVID-19

AIM

In this study, we aimed to investigate the effectiveness of ozone therapy, which is one of the integrative medicine applications that has been used safely for many years, on the prevalence of mortality in patients receiving COVID-19 treatment.

METHODS

This was a prospective, controlled study conducted on patients with COVID-19 who were hospitalised. In this study, 55 patients were included. The patients were divided into two groups as the ozone and control group. Ozone therapy (major autohemotherapy) was applied to 37 patients who were being treated with the appropriate COVID-19 treatment protocol determined by the infectious diseases committee of our hospital. The ozone treatment protocol consisted of seven sessions (one session per day) of intravenous ozone administration, applied in a volume of 100 mL and a concentration of 30 μg/mL. Only the conventional COVID-19 treatment protocol was applied to 18 patients in the control group. Clinical follow-up was performed until the discharge of the patients from the hospital with successful treatment or until the mortality occurred. Factors affecting mortality were analysed using univariate regression analysis.

RESULTS

Intensive care unit (ICU) hospitalisation was required in 6 of the 37 patients who were treated with ozone (16.2%), while 4 of 18 patients in the control group required ICU treatment (22.2%) (P = .713). When the mortality rates between the two groups were compared, mortality was lower in the ozone group (P = .032). As a result of univariate logistic regression analysis performed to investigate the factors affecting mortality, treatment with ozone therapy was determined as a risk factor for mortality. Patients receiving ozone therapy appear to have a lower mortality risk (odds ratio [OR]: 0.149, 95% confidence interval [CI] 0.026-0.863, P = .034).

CONCLUSION

In this study, the findings suggested that the administration of ozone therapy along with the conventional medical treatment in patients hospitalised for COVID-19 could reduce mortality.

Methylation of Host Genes Associated with Coronavirus Infection from Birth to 26 Years

DNA methylation (DNAm) patterns over time at 1146 CpGs on coronavirus-related genes were assessed to understand whether the varying differences in susceptibility, symptoms, and the outcomes of the SARS-CoV-2 infection in children and young adults could be explained through epigenetic alterations in a host cell’s transcriptional apparatus to coronaviruses. DNAm data from the Isle of Wight birth cohort (IOWBC) at birth, 10, 18, and 26 years of age were included. Linear mixed models with repeated measurements stratified by sex were used to examine temporal patterns, and cluster analysis was performed to identify CpGs following similar patterns. CpGs on autosomes and sex chromosomes were analyzed separately. The association of identified CpGs and expression of their genes were evaluated. Pathway enrichment analyses of the genes was conducted at FDR = 0.05. DNAm at 635 of the 1146 CpGs on autosomes showed statistically significant time effects (FDR = 0.05). The 635 CpGs were classified into five clusters with each representing a unique temporal pattern of DNAm. Of the 29 CpGs on sex chromosomes, DNAm at seven CpGs in males and eight CpGs in females showed time effects (FDR = 0.05). Sex-specific and non-specific associations of DNAm with gene expression were found at 24 and 93 CpGs, respectively. Genes which mapped the 643 CpGs represent 460 biological processes. We suggest that the observed variability in DNAm with advancing age may partially explain differing susceptibility, disease severity, and mortality of coronavirus infections among different age groups.

Immunotherapies and immunomodulatory approaches in clinical trials - a mini review

The coronavirus disease (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created havoc worldwide. Due to the non-availability of any vaccine or drugs against COVID-19, immunotherapies involving convalescent plasma, immunoglobulins, antibodies (monoclonal or polyclonal), and the use of immunomodulatory agents to enhance immunity are valuable alternative options. Cell-based therapies including natural killer cells, T cells, stem cells along with cytokines and toll-like receptors (TLRs) based therapies are also being exploited potentially against COVID-19. Future research need to strengthen the field of developing effective immunotherapeutics and immunomodulators with a thrust of providing appropriate, affordable, convenient, and cost-effective prophylactic and treatment regimens to combat global COVID-19 crisis that has led to a state of medical emergency enforcing entire countries of the world to devote their research infrastructure and manpower in tackling this pandemic.

Stability analysis and simulation of the novel Corornavirus mathematical model via the Caputo fractional-order derivative: A case study of Algeria

The novel coronavirus infectious disease (or COVID-19) almost spread widely around the world and causes a huge panic in the human population. To explore the complex dynamics of this novel infection, several mathematical epidemic models have been adopted and simulated using the statistical data of COVID-19 in various regions. In this paper, we present a new nonlinear fractional order model in the Caputo sense to analyze and simulate the dynamics of this viral disease with a case study of Algeria. Initially, after the model formulation, we utilize the well-known least square approach to estimate the model parameters from the reported COVID-19 cases in Algeria for a selected period of time. We perform the existence and uniqueness of the model solution which are proved via the Picard-Lindelöf method. We further compute the basic reproduction numbers and equilibrium points, then we explore the local and global stability of both the disease-free equilibrium point and the endemic equilibrium point. Finally, numerical results and graphical simulation are given to demonstrate the impact of various model parameters and fractional order on the disease dynamics and control.

Multi-Subunit SARS-CoV-2 Vaccine Design Using Evolutionarily Conserved T- and B- Cell Epitopes

The SARS-CoV-2 pandemic has created a public health crisis worldwide. Although vaccines against the virus are efficiently being rolled out, they are proving to be ineffective against certain emerging SARS-CoV-2 variants. The high degree of sequence similarity between SARS-CoV-2 and other human coronaviruses (HCoV) presents the opportunity for designing vaccines that may offer protection against SARS-CoV-2 and its emerging variants, with cross-protection against other HCoVs. In this study, we performed bioinformatics analyses to identify T and B cell epitopes originating from spike, membrane, nucleocapsid, and envelope protein sequences found to be evolutionarily conserved among seven major HCoVs. Evolutionary conservation of these epitopes indicates that they may have critical roles in viral fitness and are, therefore, unlikely to mutate during viral replication thus making such epitopes attractive candidates for a vaccine. Our designed vaccine construct comprises of twelve T and six B cell epitopes that are conserved among HCoVs. The vaccine is predicted to be soluble in water, stable, have a relatively long half-life, and exhibit low allergenicity and toxicity. Our docking results showed that the vaccine forms stable complex with toll-like receptor 4, while the immune simulations predicted that the vaccine may elicit strong IgG, IgM, and cytotoxic T cell responses. Therefore, from multiple perspectives, our multi-subunit vaccine design shows the potential to elicit a strong immune-protective response against SARS-CoV-2 and its emerging variants while carrying minimal risk for causing adverse effects.