Genomic epidemiology of SARS-CoV-2 in Sudan: A retrospective analysis 2020-2022 (preprint)

SARS-CoV-2 was first detected in Sudan on 13th March 2020. Here, we describe the genomic epidemiology of SARS-CoV-2 in Sudan between May 2020 and April 2022 to understand the introduction and transmission of SARS-CoV-2 variants in the country. A total of 667 SARS-CoV-2 positive samples were successfully sequenced using the nCoV-19 Artic protocol on the Oxford Nanopore Technology ([≥]70% genome completeness). The genomes were compared with a select contemporaneous global dataset to determine genetic relatedness and estimate import/export events. The genomes were classified into 37 Pango lineages within the ancestral strain (107 isolates across 13 Pango lineages), Eta variant of interest (VOI) (78 isolates in 1 lineage), Alpha variant of concern (VOC) (10 isolates in 2 lineages), Beta VOC (26 isolates in 1 lineage), Delta VOC (171 isolates across 8 lineages) and Omicron VOC (242 isolates across 12 lineages). We estimated a total of 144 introductions of the observed variants from different countries across the globe. Multiple introductions of the Eta VOI, Beta VOC and Omicron VOC were observed in Sudan mainly from Europe and Africa. These findings suggest a need for continuous genomic surveillance of SARS-CoV-2 to monitor their introduction and spread consequently inform public health measures to combat SARS-CoV-2 transmission.

Network-based integrative multi-omics approach reveals biosignatures specific to COVID-19 disease phases. (preprint)

Background: COVID-19 disease is characterized by a spectrum of disease phases (mild, moderate, and severe). Each disease phase is marked by changes in omics profiles with corresponding changes in the expression of features (biosignatures). However, integrative analysis of multiple omics data from different experiments across studies to investigate biosignatures at various disease phases is limited. Exploring an integrative multi-omics profile analysis through a network approach could be used to determine biosignatures associated with specific disease phases and enable the examination of the relationships between the biosignatures. Aim: To identify and characterize biosignatures underlying various COVID-19 disease phases in an integrative multi-omics data analysis. Method: We leveraged the correlation network approach to integrate transcriptomics, metabolomics, proteomics, and lipidomics data. The World Health Organization (WHO) Ordinal Scale (WOS) was used as a disease severity reference to harmonize COVID-19 patient metadata across two studies with independent data. A unified COVID-19 knowledge graph was constructed by assembling a disease-specific interactome from the literature and databases. Disease-state omics-specific graphs were constructed by integrating multi-omics data with the unified COVID-19 knowledge graph. We expanded on the network layers of multiXrank, a random walk with restart on multilayer network algorithm, to explore disease state omics-specific graphs and perform enrichment analysis. Results: Network analysis revealed the biosignatures involved in inducing chemokines and inflammatory responses as hubs in the severe and moderate disease phases. We observed more shared biosignatures between severe and moderate disease phases as compared to mild-moderate and mild-severe disease phases. We further identified both biosignatures that discriminate between the disease states and interactions between biosignatures that are either common between or associated with COVID-19 disease phases. Interestingly, cross-layer interactions between different omics profiles increased with disease severity. Conclusion: This study identified both biosignatures of different omics types enriched in disease-related pathways and their associated interactions that are either common between or unique to mild, moderate, and severe COVID-19. These biosignatures include molecular features that underlie the observed clinical heterogeneity of COVID-19 and emphasize the need for disease-phase-specific treatment strategies. In addition, the approach implemented here can be used for other diseases.

Impact of vaccination strategies on the spread of COVID-19 pandemics: A mathematical modelling approach (preprint)

Mathematical models with computational simulations are useful tools for analyzing the spread and control of COVID-19 disease. In this study, we develop the previous models of COVID-19 pandemics. The vaccination compartment and its reaction rates are considered. Some key computational simulations and sensitivity analysis are applied on the model. Accordingly, three techniques of sensitivity analysis are discussed to compute the local sensitivities between model states and parameters. In addition, the basic reproduction number 𝑅0 is calculated for the model equilibrium points. The elasticity between the basic reproduction number, and the model parameters is also calculated. Furthermore, the daily real data of vaccinated cases in the United Kingdom from 15th March, 2021 to 31st December, 2021 are used. Results based on sensitivity analysis show that vaccination rate, contact tracing, rapid testing are the most important parameters to reduce the basic reproduction number. This helps international efforts to reduce the number of infected individuals from the disease. Another novelty in this work is that there is a good fit between the real data and model results. The model results will provide further control strategies and help local efforts to control this disease more effectively widely.

Health-related social media use: A systematic review

Social media has been well-established in health-related purposes, especially during the COVID-19 pandemic. Preliminary reviews have summarized social media uses for a distinctive health purpose such as health interventions, health campaigns, medical education, and disease outbreak surveillance. The most recent thorough review of social media uses for health purposes, however, was conducted in 2013. A systematic review that covers various health purposes is needed to reveal the new usages and research gaps that emerge in recent years. This study aimed to provide a systematic review of social media uses for health purposes that have been identified in previous studies. The researchers searched for peer-reviewed journal articles published between 2010 and 2020 in.10 databases covering medicine, public health, and social science. After classifying the articles in terms of publication year, journal area, country, method, social media platform, and social media use for health purposes, the researchers provided a review of social media use for health purposes identified in these articles. This study summarized 7 social media uses for various health purposes by health organizations, health researchers and practitioners, and the public. Social media can be used for various health purposes. Several new usages have emerged since 2013 including advancing health research and practice, social mobilization, and facilitating offline health-related services and events. Research gaps exist regarding advancing strategic use of social media based on audience segmentation, understanding the impact of health identity development, and addressing privacy concerns and evaluating the impact of social media in health interventions. © 2023 Author(s).

Study of pulmonary hypertension in post-COVID-19 patients by transthoracic echocardiography

BackgroundA devastating medical disorder, the coronavirus pandemic infection (COVID-19), produced by the coronavirus 2 (SARSCoV-2), is primarily characterized by severe pneumonia. Pulmonary hypertension (PH), which may cause right ventricular (RV) involvement and dysfunction, can occur as a result of lung parenchymal injury and disturbed pulmonary circulation. Transthoracic echocardiography (TTE) is a very reliable noninvasive approach to determining the severity of PH. Similar to that, thorax computer tomography (TCT) can effectively detect the severity of lung damage during the acute phase of a COVID-19 infection.AimsThe goal of this research is to examine PH and altered right ventricular function by TTE in post-COVID-19 cases.Patients and methodsThis retrospective case-control study was conducted at Tanta Chest University Hospital, Tanta, Egypt. The study started from October 2021 to September 2022 on 50 post-COVID-19 cases with one or more clinical manifestations of PH. These cases underwent TTE (group I showed normal PAP "control group," groups II & III with PH further subdivided according to PaO2).ResultsRisk factors of age, BMI, diabetes mellitus, and smoking were substantially raised in group III, but sex and hypertension were insignificant. Symptoms of chest pain, dyspnea, and palpitation were worse in group III. Levels of LDH, d-dimer, ESR, and serum bilirubin were substantially increased in group III in comparison to the other groups. Post-COVID-19-associated lung fibrosis and embolism were higher in group III. Mean values of estimated systolic pulmonary artery pressure (esPAP) and right atrial and right ventricular diameters were substantially increased in groups III and II in comparison to group I. Mean values of RV-GLS and TAPSE were lower in groups III and II in comparison to group I. FEV1, FVC, PEFR, and FEF25-75% percentage of the predicted were significantly low in groups II and III. FEV1/FVC ratio was substantially lower in group II in comparison to groups I and III.ConclusionsThe incidence of pulmonary hypertension in post-COVID-19 patients with suspected manifestations of PH is 70%. Increased age, BMI, DM, smoking, decreased PaO2, increased CORADS score, and abnormal spirometry are risk factors for PH in post-COVID-19 patients. Patients with post-COVID-19 PH stay more either in ICU or ward.

Masked Face Recognition Model with Explainable AI

Due to the recent COVID-19 pandemic, people tend to wear masks indoors and outdoors. Therefore, systems with face recognition, such as FaceID, showed a tendency of decline in accuracy. Consequently, many studies and research were held to improve the accuracy of the recognition system between masked faces. Most of them targeted to enhance dataset and restrained the models to get reasonable accuracies. However, not much research was held to explain the reasons for the enhancement of the accuracy. Therefore, we focused on finding an explainable reason for the improvement of the model's accuracy. First, we could see that the accuracy has actually increased after training with a masked dataset by 12.86%. Then we applied Explainable AI (XAI) to see whether the model has really focused on the regions of interest. Our approach showed through the generated heatmaps that difference in the data of the training models make difference in range of focus. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.

A Mathematical Study for the Transmission of Coronavirus Disease

Globally, the COVID-19 pandemic's development has presented significant societal and economic challenges. The carriers of COVID-19 transmission have also been identified as asymptomatic infected people. Yet, most epidemic models do not consider their impact when accounting for the disease's indirect transmission. This study suggested and investigated a mathematical model replicating the spread of coronavirus disease among asymptomatic infected people. A study was conducted on every aspect of the system's solution. The equilibrium points and the basic reproduction number were computed. The endemic equilibrium point and the disease-free equilibrium point had both undergone local stability analyses. A geometric technique was used to look into the global dynamics of the endemic point, whereas the Castillo-Chavez theorem was used to look into the global stability of the disease-free point. The system's transcritical bifurcation at the disease-free point was discovered to exist. The system parameters were changed using the basic reproduction number's sensitivity technique. Ultimately, a numerical simulation was used to apply the model to the population of Iraq in order to validate the findings and define the factors that regulate illness breakout.

Medical staff engagement in public hospital: The role of citizenship behaviour and trust during COVID-19 pandemic

The purpose of conducting this study is to examine the effect of employee citizenship behaviour and trust on employee engagement among medical staff in one of public hospital located in the Northern Region of Malaysia. This research is carried out by using a quantitative method through the distribution of the self-directed questionnaires. Simple random sampling is utilised in this research. The sample size consisted of 160 medical staff who have participated voluntarily to involve in the study. Based on the multiple regression analysis, results presented a significant effect of citizenship behaviour on employee engagement (β=.55, t=8.07, p=.00) among medical staff in this institution. Similarly, a significant effect of trust on medical staff engagement (β=.49, t=3.34, p=.00) is presented in this study. In the current scenario, the public health institutions should actively penetrate the elements of citizenship and trust in order to remain the desired level of medical staff engagement during the COVID-19 pandemic. © 2023 Author(s).

Deep learning-based COVID-19 diagnosis using CT scans with laboratory and physiological parameters

The global economy has been dramatically impacted by COVID-19, which has spread to be a pandemic. COVID-19 virus affects the respiratory system, causing difficulty breathing in the patient. It is crucial to identify and treat infections as soon as possible. Traditional diagnostic reverse transcription-polymerase chain reaction (RT-PCR) methods require more time to find the infection. A high infection rate, slow laboratory analysis, and delayed test results caused the widespread and uncontrolled spread of the disease. This study aims to diagnose the COVID-19 epidemic by leveraging a modified convolutional neural network (CNN) to quickly and safely predict the disease's appearance from computed tomography (CT) scan images and a laboratory and physiological parameters dataset. A dataset representing 500 patients was used to train, test, and validate the CNN model with results in detecting COVID-19 having an accuracy, sensitivity, specificity, and F1-score of 99.33%, 99.09%, 99.52%, and 99.24%, respectively. These experimental results suggest that our strategy performs better than previously published approaches.

Assessment of the Impact of the Egyvir on Rats Experimental Animals, a Preclinical Study for Sars-Cov-2 Treatment

Background: The SARS-COV-2 is a worldwide pandemic problem. We developed a herbal extract with potent in-vitro virucidal, anti-inflammatory and immunomodulatory effects called EGIVIR. Our aim is to assess the bioavailability and cytotoxicity of EGYVIR on different organs and biological systems in Sprague Dawley rats as a model of experimental animals.Methods: 128 rats were divided into 16 groups (8 rats each), where Egyvir was assessed in oral doses of 20, 30, and 40 mg/kg body weight, and by inhalation in 0.2, 0.3, and 0.4 mg/kg body weight, four times/day, compared to the control groups.Results: The Egyvir had no significant effect on the blood pressure, pulse, motor activity, histological, hematological, and coagulation profiles. Also, the blood levels of triglycerides, cholesterol, blood glucose, lactate dehydrogenase (LDH), and creatine phosphor kinase (CPK) were not significantly affected. Egyvir had no harmful effect on the kidney and liver functions, blood electrolytes levels and urinary levels of sodium, potassium, and chloride. There was no significant effect on the serum levels of interleukin-113 (IL -113), IL-2, IL-4, IL-6, IL-10, interferon-gamma (IFN-gamma), and tumor necrosis factor-alpha (TNF-alpha). Additionally, there was no significant change in the levels of Superoxide dismutase (SOD), catalase, reduced glutathione (GSH), and malonaldehyde (MDA) in comparison to the control groups (P<0.05).Conclusion: Egyvir is considered a safe antiviral natural drug. It could be used for the treatment of SARS-COV-2 without any adverse effects when used with the recommended doses. However, these data are a preliminary step for validation in a clinical setting.

Mainstreaming disaster risk management technical and vocational education and training (DRM-TVET) program in higher education institutions: flexible ladderized capacity building model amid COVID-19

Disasters are increasingly becoming more destructive in their impacts. Lives have been lost and properties damaged due to the lack of institutional and personnel coping and adaptive capacities. Several policies in the Philippines have noted the importance of capacity development in implementing Disaster Risk Management (DRM). To meet the above necessity, in 2017, Philippine School of Business Administration (PSBA), Manila, one of the higher education institutions pioneered a specialization of DRM in its existing Master in Business Administration program. However, meeting the demand for Disaster Risk Management Technical and Vocational Education and Training (DRM-TVET) through Formal Degree Program (FDP) and keeping FDP sustainable is still facing a number of challenges. The main drivers of these challenges include but are not limited to the following: time constraint on the part of participants to complete 2–4 years' FDP;lack of institutions offering DRM-TVET programs;and unavailability of a Learning Management System. The main objective of this research is to develop an Alpha-Flexible Ladderized Capacity Building Model (A-FLCBM) amid COVID-19. Further, the study should also provide logical flow and recommendations to operationalize the remaining activities of the Conceptual Framework in developing the Beta (B)-FLCBM amidst COVID-19. In this regard, the researchers collected pertinent data through a substantive, thorough, sophisticated literature review and examined the available mandates on existing Flexible ladderized models. Further, a Conceptual Framework (CF) is also developed and partially operationalized. The output allowed researchers to develop A- FLCBM amidst COVID-19 using the PSBA curriculum as a pilot case. However, the framework activities, i.e., dry run, Technical Education and Skills Development Authority (TESDA) registration for National Certification (NC), development of B-FLCBM, and the empirical assessment of DRM-TVET and FDP sustainability will be covered in future studies. The A-FLCBM comprises of interrelated activities including mode of learning and well-designed DRM NC short courses, workshops, and trainings for the trainers. The Model is aligned with the Executive Order 358, promulgated in 2004. Further, the Ladderized Education (LE) system introduced through Commission on Higher Education Memorandum Order No. 43, 2008 Series, was also considered for wider-scale and accelerated implementation of LE nationwide and globally. The implementation of B-FLCBM will provide a unique opportunity to develop the skills required to be a professional in the DRM and business continuity field, improving the quality of life and raising awareness on the importance of preventing and mitigating disasters and reducing the loss incurred by countries in terms of lives, property, and economy. © 2023 Elsevier Inc. All rights reserved.

Recent patents for handling Covid-19: Snapshot from Indonesian patent database

In recent years, the world in fear due to covid-19 outbreaks which impacted to the all aspect of life. As a many other countries, Indonesia with huge population consider to handle the spread the covid-19 through develop the innovation and technologies that highly related to the patent. This study aims to present the descriptive examination of the patent landscape related to the Covid-19 in Indonesia. Furthermore, the information of patent application obtains from Indonesian patent database and classified by the selected categories. This study reveals that the Research, Development, and Innovation (RDI) activities dominated by the Indonesian higher education. The highest filling date in December 2020 highly correlated with the obliged research outcome that funded research by the Indonesian Government. Additionally, the patent classifying by the type of method, process, tools, and products and there's no significant distinction number among the types. © 2023 Author(s).

A Systematic Review on the Biophilic Designs for Home Workspace during the Covid-19 Quarantine

Research on biophilic design succumbs the built environment can become recuperative with the presence of natural elements. Most of studies on biophilic designs were based on outdoor environment, office buildings, and also child play and learning spaces. Yet, less emphasis has been given on biophilic designs regarding home workspace settings particularly the academic staffs who are working from home due to the sudden shift from working in office to working from home because of the Covid-19 pandemic. Hence, this study was set out to analyze the existing literature on the elements of the biophilia and its design strategies specifically for home workspace settings. Guided by PRISMA review method, nine related studies out of thirty-seven documents were identified from the Web of Science and the Scopus databases searches. Further review of these articles had resulted in three main themes of biophilic design settings specifically for home workspace settings. They were direct involvement of nature, indirect involvement of nature and involvement of space and place. For further research, these three themes could contribute in the development of a comprehensive biophilic design elements model for home workspace setting towards the attention restoration and the stress reduction among occupants. © 2023 American Institute of Physics Inc.. All rights reserved.

Impact of Covid-19 on Mental Health among Medical Students

Background: The COVID-19 pandemic is a major health crisis affecting several nations. Such widespread outbreaks are associated with adverse mental health consequences. Objective(s): To conduct a survey-based assessment of mental health among medical students during the COVID-19 pandemic. Aimed at identifying severity levels of depression and anxiety, stressors related to the pandemic, and barriers students experienced in handling the pandemic-related stress. Method(s): An analytical cross-sectional study was chosen as the study design for this research to study the association between demographic social and mental health among medical students during the pandemic COVID-19. Result(s): The results of this study were collected by respondents through questionnaires as the respondents were needed to answer about 16 questions and the main question was asked mostly about their mental health condition during the pandemic COVID-19. 101 respondents participated in the study. Discussion(s): the impact of COVID-19 on mental health among medical students has been studied. Due to the long-lasting pandemic situation and numerous measures such as lockdown and stay-at-home orders, COVID-19 brings negative impacts on higher education of medical students, self and social isolation, disconnection from friends and teachers resulting in more medical students than ever experiencing feelings of helplessness, isolation, grief, anxiety and depression. The issue of mental health is not only relevant but crucial. Demand for health support services has increased exponentially as a result. Conclusion(s): In this study, severity levels of depression and anxiety, stressors related to the pandemic, and barriers students experienced in handling the pandemic-related stress have increased due to many factors such as social isolation, own health and the health of loved ones, financial difficulties, suicidal thoughts, depressive thoughts, class workload, changes in living environment, eating patterns and sleeping habits.Copyright © RJPT. All right reserved.

Knowledge, attitude and practices of teledentistry during the COVID-19 pandemic in Southern Saudi Arabia

Aim: The aim of this study was to assess the knowledge, attitudes and practice of teledentistry during COVID-19 among dentists in Southern Saudi Arabia. Material(s) and Method(s): A questionnaire with 27 questions was constructed, validated and circulated electronically via social media channels like WhatsApp and by email to dentists from various fields in Southern Saudi Arabia. Data were collected and analyzed using the statistical software SPSS 23.0. Result(s): Most of the respondents showed a positive behavior towards all domains of the questionnaire, including knowledge, attitude and practice of teledentistry. Out of 839 participants, 532 participants were familiar with this term, most of them (64.4%) were practicing it during the pandemic of COVID-19. Discussion(s): It is an emerging technique that has the ability to improve the delivery of dental care diagnosis to communities with limited access or no access to specialists. As of today, there is a need for improvement in practicing it among the Saudi dental community.Copyright © 2022, Derman Medical Publishing. All rights reserved.

Comparison of Diagnostic Accuracy of CRP Versus Ferritin in COVID Patients as a Marker of Severity of Disease Taking who Severity Classification as Gold Standard

Objective: To determine the diagnostic accuracy of elevated C reactive protein (CRP) and ferritin in predicting severe Covid-19 infection using the World Health Organization's (WHO) Covid-19 severity classification as gold standard. Study Design: Descriptive study. Place and Duration of Study: This study was conducted at the Pak Emirates Military Hospital, Rawalpindi, from January 1st 2021 till April 30th 2021. Ethical review committee's (ERC) approval was taken and good clinical practice guidelines were followed. Material(s) and Method(s): Baseline blood samples were sent to the hospital laboratory for the measurement of C reactive protein and ferritin levels. PCR was taken as gold standard for the diagnosis of Corona virus disease. Patients were classified into severe and non-severe categories using WHO classification of severity. Sensitivity, specificity, diagnostic accuracy, negative predictive value and positive predictive value were calculated for elevated CRP and ferritin. Result(s): There were 65 (57.5%) patients who had severe Covid-19 disease and 48 (42.5%) patients who had non-severe Covid-19 disease. Among the patients with severe Covid-19, 57 (87.7%) had elevated CRP levels, and 50 (76.9%) patients had elevated ferritin levels. Testing ferritin levels, against the severity of Covid-19 patients, there was a sensitivity of 76.9%, specificity of 79.2%, positive predictive value (PPV) of 83.3%, negative predictive value (NPV) of 71.7% and diagnostic accuracy of 77.8%. Testing CRP levels, there was a sensitivity of 87.7%, specificity of 85.4%, PPV of 89.1%, NPV of 83.6% and diagnostic accuracy of 86.7%. Conclusion(s): The results from our study show that CRP has a slightly improved diagnostic accuracy as compared to ferritin. However, both these markers have value in the prediction of severity of Covid-19 infection.Copyright © 2023 Lahore Medical And Dental College. All rights reserved.

The comparison of Zoom meeting and Google Meet acceptance toward the online learning using TAM method

The COVID-19 pandemic has an impact on all sectors, including the education sector, which has led to policies for learning from home or distance learning (pjj) as an alternative to learning at all levels of education. Many applications have emerged that can support online learning, some of which are the online meeting application Zoom and Google Meet. However, the use of this supporting application still needs to be researched to see that this application is more effective in terms of usability according to user perceptions. For this reason, researchers used the TAM (Technology Acceptance Model) model to measure the quality of the two applications by using five variables or model constructs from the TAM research model, namely Actual System Use, Attitude Toward Using, Behavioral Intention of Use, Peceived Ease of Use and Perceived Usefulness. In this study, researchers used a Google Form questionnaire for data collection based on purposive sampling technique. With this technique, the researcher determines the sample only for Bina Sarana Informatika University Margonda Campus students who use Zoom Cloud Meeting and Google Meet for PJJ media. Researchers also use the Slovin formula in determining the minimum sample size with a standard error of 5%. Based on the total population of 143 and producing a minimum sample size of 105. Researchers used data with a sample size of 111 with 79 male respondents and 32 female respondents. Based on the results of research using this TAM, the results obtained if all google meet hypotheses are accepted while one hypothesis of zoom meeting is rejected. The hypothesis is rejected indicating that the Perceived Benefit has no effect on the Intention of Use Behavior. So that the conclusion is that students are more interested in Google Meet as an online learning medium other than face-to-face compared to Zoom Meeting. © 2023 Author(s).

Biochemical and hematological variables in COVID-19 positive patients

The coronavirus disease 2019 (COVID-19) pandemic has introduced attention to request for various diagnostic strategies, comparative validation of novel tests, quicker federal agency clearance, and quick manufacture of test kits to satisfy worldwide demand. Thus, this study was aimed to investigate biochemical and hematological variables in COVID-19 positive patients, so as to act early and improve patient outcomes. 34 patients with COVID-19 patients were diagnosed at Rifai General Hospital, Dhi Qar Health Directorate, during the period of (15 September 2020 to March 2021) in this study with two study group, as group one (i.e. the first week infection) and group two (i.e. the second week infection). The reagents kits for Random Blood Sugar (RBS) were used, and also urea, and creatinine measurements were done by spectrophotometry method (Biolabo/France), whereas D-dimer measurement was performed by)MAGLUMI 1000-China), Complete Blood Count measurement was conducted by XP-300™ Automated Hematology Analyzer System Device, USA. In this study, it was found that WBC had a significant difference (p-value 0.05) based on the comparison between the two groups, whereas RBS and creatinine had no significant difference (p-value>0.05) and urea and D-dimer had a significant difference (p-value 0.05) when compared between the two groups. The D-dimer and urea levels were significantly increased in the second group compared with the first group of the patients. Copyright © 2023 by SPC (Sami Publishing Company)