Whole-Exome Sequencing Detecting a Recurrent Pathogenic Mutation, HFE p.His63Asp (H63D) in COVID-19 Patients and Its Effect on Mortality.

BACKGROUND: In recent years, various coronaviruses have caused severe respiratory illnesses worldwide. For example the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections of COVID-19 outbreak in 2019 in Wuhan, China. Genome-wide association studies (GWAS) have significantly expanded our comprehension of how specific genetic variations are linked to diseases. Research has demonstrated the existence of genetic factors influencing susceptibility to coronaviruses. The objective of this study was to examine the association of certain loci with the COVID-19 in Saudi population. METHODS: In the present study we have examined the link between the COVID-19 disease and certain genetic variants in hospitalized COVID-19 patients (n = 16) in Tabuk and Bisha, Kingdom Saudi Arabia. We used the genome Analysis Toolkit (GATK) and Comprehensive variant annotation was performed different databases and tools such as Search Tool for the Retrieval of Interacting Genes (STRING), PanelApp and PolyPhen-2. RESULTS: The study showed that the genetic variants associated with genes such as Homeostatic Iron Regulator (HFE) (found in 7 patients, representing 44%), complement factor H (CFH) (6 patients, 38%), cadherin 23 (CDH23) (4 patients, 25%), cytotoxic T-lymphocyte associated protein 4 (CTLA-4) (3 patients, 19%), Transforming Growth Factor Beta 1 (TGFB1) (3 patients, 19%), CREB-binding protein (CREBBP) (2 patients, 13%), E1A Binding Protein P300 (EP300) (2 patients, 13%), hemoglobin subunit beta (HBB) (2 patients, 13%), interferon regulatory factor 7 (IRF7) (2 patients, 13%), and unc-119 lipid binding chaperone (UNC119) (2 patients, 13%) might be associated with susceptibility to coronavirus. We also identified mutations in the COVID-19 patient that are pathogenic or likely pathogenic. CONCLUSION: A recurrent pathogenic mutation, HFE p.His63Asp (H63D), was identified in 7 patients, suggesting its potential contribution to disease severity. Additionally, a likely pathogenic variant, HBB p.Glu7Val (E7V), was present in 2 patients, highlighting its potential role in disease susceptibility. Our results shed light on the key genetic mechanisms of COVID-19 pathogenesis and help to identify and stratify the individuals or populations that are at risk to corona virus infection. The identification of susceptible individuals or populations assist in prevention and/or in treatment programs.

Molecular Determination of Tumor Necrosis Factor-alpha, Interleukin-8, Interleukin-10, and C-X-C Chemokine Receptor-2 Genetic Variations and their Association with Disease Susceptibility and Mortality in COVID-19 Patients.

Background: Altered cytokine levels have been associated with poor outcomes among COVID-19 patients. TNF-α, IL-8 and IL-10 are key cytokines in COVID-19 pathogenesis, and CXCR-2 is a major chemokine receptor involved in inflammatory response. Polymorphisms in the genes of these proteins are proposed to influence disease outcomes. In this study, we aimed to find out the association of genetic polymorphisms in TNF-α, IL-8, IL-10 and CXCR-2 genes with susceptibility to and mortality of COVID-19. Methods: The present case-control study was conducted on 230 subjects, among whom 115 were clinically diagnosed and RT-PCR-confirmed COVID-19 patients and 115 healthy control subjects. The polymorphisms in TNFα -308 G>A (rs1800629), IL-8 -251T>A (rs4073), CXCR2 +785 C>T (rs2230054) genes were detected by ARMS -PCR assay whereas for IL-10 (-1082 G>A), rs1800896 G>A allele-specific PCR assay was used and their association with COVID-19 susceptibility and mortality was estimated by multivariate analysis. The results were analyzed for risk of infection and mortality through different inheritance models. Results: Frequencies of TNF-α rs1800629 GA, AA, IL-8 rs4073 TA, AA, IL-10 (-1082 G>A), rs1800896 GA and GG, and CXCR2 rs2230054 CT genotypes were significantly higher in COVID-19 patients compared to the control group (p < 0.05). Furthermore, COVID-19 patients had a higher frequency of the polymorphic A allele of TNF-α, the A allele of IL-8, the G allele of IL-10, and the T allele of CXCR2. The risk of susceptibility to COVID-19 was significantly associated with TNF-α rs1800629 GA, GA+AA genotypes and the A allele, IL-8 rs4073 TA, AA genotypes and A allele, IL-10 rs1800872 GA and CC genotypes and C allele, and CXCR2 rs2230054 CT and CT+CC genotypes. TNF-α-GA and AA genotypes and A allele, IL-8 TA and AA genotypes and A allele and CXCR-2 CC and CT genotypes have significant associations with mortality risk in COVID-19 patients, while GA and GG genotypes of the IL-10 are shown to confer significant protection against mortality from COVID-19. Conclusion: The findings of this study provide important insights into the COVID-19 disease and susceptibility risk. The polymorphisms in TNFα -308 G>A (rs1800629), IL-8 -251T>A (rs4073), IL-10 (-1082 G>A), rs1800896 and CXCR2 +785 C>T (rs2230054) are associated with the risk of susceptibility to COVID-19 and with mortality in COVID-19 patients. Further studies with larger sample sizes are necessary to confirm our findings.

An Observational Pilot Study of a Tailored Environmental Monitoring and Alert System for Improved Management of Chronic Respiratory Diseases.

Objective: Chronic lung-related diseases, with asthma being the most prominent example, characterized by diverse symptoms and triggers, present significant challenges in disease management and prediction of exacerbations across patients. This research aimed to devise a practical solution by introducing a personalized alert system tailored to individual lung function and environmental conditions, offering a holistic approach for the management of a range of chronic respiratory conditions. Methods: In response to these challenges, we developed a personalized alert system based on individual lung function tests conducted in diverse environmental conditions, as determined by air-quality sensors. Our research was substantiated through an observational pilot study involving twelve healthy participants. These participants were exposed to varying air quality, temperature, and humidity conditions, and their lung function, as indicated by peak expiratory flow (PEF) values, was monitored. Results: The study revealed pronounced variability in pulmonary responses across different environments. Leveraging these findings, we proposed a design of a personalized alarm system that monitors air quality in real-time and issues alerts under potentially unfavorable environmental conditions. Additionally, we investigated the use of basic machine learning techniques to predict PEF values in these varied environmental settings. Discussion: The proposed system offers a proactive approach for individuals, particularly those with asthma, to actively manage their respiratory health. By providing real-time monitoring and personalized alerts, it aims to minimize exposure to potential asthma triggers. Ultimately, our system seeks to empower individuals with the tools for timely intervention, potentially reducing discomfort and enhancing management of asthma symptoms.

Curriculum Mapping for Curriculum Development: The Notion of "Curriculum Barcoding" in View of the Saudi Medical Education Directives Framework (SaudiMEDs).

Objectives This study aims to map the curriculum of the Faculty of Medicine at Tabuk University to assess its comparability with the SaudiMEDs competency framework. Methodology We developed a checklist based on the essential clinical presentations and skills listed in the SaudiMEDs to map our curriculum and determine the comparability. This cross-sectional descriptive study started on 1 September 2015 until 29 February 2016. The coordinators of the 34 modules completed the checklist and identified whether each clinical presentation or skill is taught in their relevant modules. Results Results showed that our curriculum is lacking in 3.9% of the clinical presentations and 23.9% of the skills deemed necessary by the SaudiMEDs, and require attention. Deficient skills were mainly hospital-based ones. The project yielded a content "expertise" map regarding where the main domains of knowledge and skills in the SaudiMEDs framework are addressed in our curriculum. The "SaudiMEDs barcode" is generated that we hypothesize as a novel method for the description of our program in relation to the national competency framework.  Conclusion Curriculum mapping is a powerful tool for curriculum improvement. Our study elucidated a minor gap in the knowledge domains but a significant one in the essential skills in relation to the SaudiMEDs. We recommend structured training during the internship period as an essential supplement to undergraduate medical qualifications. During our experimentation with curriculum mapping, we articulated the "SaudiMEDs barcode" that we suggest as a novel method for curriculum alignment to the matrix of national competency and, hopefully, to aid in the accreditation projects.

IL-2 and IL-1ß Patient Immune Responses Are Critical Factors in SARS-CoV-2 Infection Outcomes.

BACKGROUND: Immune dysregulation has been linked to morbidity and mortality in COVID-19 patients. Understanding the immunology of COVID-19 is critical for developing effective therapies, diagnostics, and prophylactic strategies to control the disease. AIM: The aim of this study was to correlate cytokine and chemokine serum levels with COVID-19 disease severity and mortality. SUBJECTS AND METHODS: A total of 60 hospitalized patients from the Tabuk region of Saudi Arabia with confirmed COVID-19 were included in the study. At hospital admission, the IL-1 ß, IL-2, IL-8, IL-10, LT-B4, and CCL-2 serum levels were measured. The cytokine levels in COVID-19 patients were compared to the levels in 30 healthy matched control subjects. RESULTS: The IL-1 ß, IL-2, LTB-4, CCL-2, and IL-8 levels (but not IL-10) were significantly higher in all COVID-19 patients (47 survivors and 13 non-survivors) compared with the levels in the healthy control group. In the non-survivor COVID-19 patients, patients' age, D-dimer, and creatinine kinase were significantly higher, and IL-1 ß, IL-2, and IL-8 were significantly lower compared with the levels in the survivors. CONCLUSION: Mortality rates in COVID-19 patients are associated with increased age and a failure to mount an effective immune response rather than developing a cytokine storm. These results warrant the personalized treatment of COVID-19 patients based on cytokine profiling.

Severe COVID-19 Pneumonia and Genetic Susceptibility: A Case Report and Literature Review.

Genetic susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) morbidity and mortality continues to evolve. This report presents a case of an apparently healthy male adult who developed severe coronavirus disease 2019 (COVID-19) and a study on relevant genetic mutations, namely, angiotensin-converting enzyme 2 (ACE2-rs4646994 I/D) gene, glutathione S-transferase (GST) M1 and T1 gene, and miR-423 rs6505162 C>A gene polymorphism. Results showed that the ACE-DD genotype of ACE2, (GSTM1+/+) (GSTT1-/-) genotype of GST gene, and CA genotype (heterozygosity) of miR-423 rs6505162 genes, which were found in the patient, could be independent risk factors of severe COVID-19, even without comorbidities.