Frequency of HLA alleles among COVID-19 infected patients: Preliminary data from Saudi Arabia.
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ABSTRACT:
SUBMITTER: Naemi FMA
PROVIDER: S-EPMC8100873 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Human leukocyte antigens (HLA) diversity has a tremendous impact on shaping the transplantation practices, transfusion-associated graft versus host disease prevention strategies, and host–pathogen interactions. Here, we conducted a retrospective study of HLA class I and class II homozygosity at allelic and haplotype levels in unrelated individuals genotyped from 2012 to 2016 in a tertiary hospital in the capital of Saudi Arabia. Among 5,000 individuals, 2,773 individuals meet inclusion criteria and were retrospectively analyzed for HLA-A, -B, -C–DRB1, and -DQB1 homozygosity at allelic and haplotype levels. HLA molecular typing was performed using a commercial reverse sequence-specific oligonucleotide (rSSO) kit. We were able to identify 15 HLA-A, 20 HLA-B, 11 HLA-C, 13 HLA-DRB1, and five HLA-DQB1 homozygous alleles demonstrating a very low genetic diversity in the Saudi population. The highest homozygosity in HLA class I was found in locus C followed by A and B (20.3% > 16.1% > 15.5%; p < 0.001) where the most homozygote alleles were A*02 (9.2%), B*51 and B*50 (5.7% and 3.7%), and C*07, C*06, and C*15 (7.2%, 5.48%, and 3.3%) and in HLA class II, the highest homozygosity was found in locus DQB1 compared to DRB1 (31.71% > 19.2%; p < 0.001), with the most common homozygote alleles being DRB1*07 and DRB1*04 (5.33% and 4.2%) and DQB1*02, DQB1*06, and DQB1*03 (13.55%, 7.92%, and 7.64%). The frequency of finding an individual with one homozygote allele was (24.6%), two homozygote alleles (13.5%), three homozygote alleles (4.7%), four homozygote alleles (3.4%), and five alleles were (4.8%). The most frequent homozygote haplotypes are A*23∼C*06∼B*50∼DRB1*07∼DQB1*02 and A*02∼C*06∼B*50∼DRB1*07∼DQB1*02. This study shows low diversity of both class I and II alleles and haplotypes in the Saudi population, which would have a significant impact on shaping the transplantation practices, transfusion-associated graft versus host disease prevention strategies, and host–pathogen interactions.
| S-EPMC9218871 | biostudies-literature
Project description:IntroductionHuman leukocyte antigen (HLA) variability has been demonstrated to be associated with susceptibility/severity of COVID-19. High-resolution HLA genotyping to identify alleles associated with severe COVID-19 in an Indian cohort was performed.MethodsQuantitative reverse-transcription polymerase chain reaction-confirmed SARS-CoV-2-positive patients with mild/moderate/severe disease (n = 54) and asymptomatic (n = 42) were recruited and genotyped for 11-HLA loci on MiSeq using NGSgo®-MX11-3 and analyzed (NGSengine; GenDx).ResultsA significant difference in alleles between the groups was identified for HLA-C*04:01:01:01, HLA-DRB5*01:01:01:02, HLA-DQA1*03:01:01:01, HLA-DPB1*04:01:01:41, and HLA-DPA1*01:03:01:02. Alleles namely, HLA-C*04:01:01:01 (OR: 5.71; 95% CI: 1.2-27.14; p = .02), HLA-DRB5*01:01:01:02 (OR: 2.94; 95% CI: 1.1-7.84; p = .03), DQA1*03:01:01:01 (OR: 22.47; 95% CI: 1.28-393.5; p = .03), HLA-DPB1*04:01:01:41 (OR: 9.44; 95% CI: 0.5-175.81; p = .13), and HLA-DPA1*01:03:01:02 (OR: 8.27; 95% CI: 2.26-30.21; p = .001) were associated with severe COVID-19.ConclusionGenotyping for these alleles will enable identification of individuals at risk of severe disease and stratification for preferential vaccination.
| S-EPMC8426675 | biostudies-literature
Project description:BACKGROUND:The first case of COVID-19 in Saudi Arabia was confirmed on March 3, 2020. Saudi Arabia, like many other countries worldwide, implemented lockdown of most public and private services in response to the pandemic and established population movement restrictions nationwide. With the implementation of these strict mitigation regulations, technology and digital solutions have enabled the provision of essential services. OBJECTIVE:The aim of this paper is to highlight how Saudi Arabia has used digital technology during the COVID-19 pandemic in the domains of public health, health care services, education, telecommunication, commerce, and risk communication. METHODS:We documented the use of digital technology in Saudi Arabia during the pandemic using publicly available official announcements, press briefings and releases, news clips, published data, peer-reviewed literature, and professional discussions. RESULTS:Saudi Arabia's government and private sectors combined developed and launched approximately 19 apps and platforms that serve public health functions and provide health care services. A detailed account of each is provided. Education processes continued using an established electronic learning infrastructure with a promising direction toward wider adoption in the future. Telecommunication companies exhibited smooth collaboration as well as innovative initiatives to support ongoing efforts. Risk communication activities using social media, websites, and SMS text messaging followed best practice guides. CONCLUSIONS:The Saudi Vision 2030 framework, released in 2017, has paved the path for digital transformation. COVID-19 enabled the promotion and testing of this transition. In Saudi Arabia, the use of artificial intelligence in integrating different data sources during future outbreaks could be further explored. Also, decreasing the number of mobile apps and merging their functions could increase and facilitate their use.
| S-EPMC7473704 | biostudies-literature
Project description:Background: COVID-19 virus has been reported as a pandemic in March 2020 by the WHO. Having a balanced and healthy diet routine can help boost the immune system, which is essential in fighting viruses. Public Health officials enforced lockdown for residents resulting in dietary habits change to combat sudden changes. Design and Methods: A cross-sectional study was conducted through an online survey to describe the impact of the COVID-19 pandemic on the eating habits, quality and quantity of food intake among adults in Saudi Arabia. SPSS version 24 was used to analyze the data. Comparison between general dietary habits before and during COVID-19 for ordinal variables was performed by Wilcoxon Signed Rank test, while McNemar test was performed for nominal variables. The paired samples t-test was used to compare the total scores for food quality and quantity before and during COVID-19 periods. Results: 2706 adults residing in Riyadh completed the survey. The majority (85.6%) of the respondents reported eating homecooked meals on a daily basis during COVID-19 as compared to 35.6% before (p<0.001). The mean score for the quality of food intake was slightly higher (p=0.002) before the COVID-19 period (16.46±2.84) as compared to the during period (16.39±2.79). The quantity of food mean score was higher (p<0.001) during the COVID-19 period (15.70±2.66) as compared to the before period (14.62±2.71). Conclusion: Dietary habits have changed significantly during the COVID-19 pandemic among Riyadh residents. Although some good habits increased, the quality and the quantity of the food was compromised. Public Health officials must focus on increased awareness on healthy eating during pandemics to avoid negative consequences. Future research is recommended to better understand the change in dietary habits during pandemics using a detailed food frequency questionnaire. Significance for public health Since pandemics come unannounced affecting public’s safety, it is important to understand the changes that occur in a community. This study focuses on the dietary habits’ changes during the COVID-19 pandemic. Coronavirus has been a threatening matter on a global level. It is tremendously crucial to consider various aspects of human health during pandemics including dietary habits, food quality and quantity as such factors play an important role in improving the immune system and overall health. Increasing the community’s awareness on the importance of healthy food intake during COVID-19 pandemic is extremely necessary. Public health’s role is to understand people’s reactions during pandemics and establish guidelines to improve health and prevent diseases. Dietary habits change during COVID-19 is a major health threat that needs immediate Public Health Officials’ attention. Maximizing awareness about healthy eating habits during quarantine requires attention to improve the overall health of the population.
| S-EPMC7512943 | biostudies-literature
Project description:BackgroundSpinal Muscular Dystrophy (SMA) is one of the leading causes of death in infants and young children from heritable diseases. Although no large-scale popultion-based studies have been done in Saudi Arabia, it is reported that the incidence of SMA is higher in the Saudi population partly because of the high degree of consanguineous marriages.MethodsThe final analysis included 4198 normal volunteers aged between 18 and 25 years old, 54.7% males, and 45.3% females. Whole blood was spotted directly from finger pricks onto IsoCode StixTM and genomic DNA was isolated using one triangle from the machine. To discern the SMN1 copy number independently from SMN2, Multiplex PCR with Dral restriction fragment analysis was completed. We used the carrier frequency and population-level data to estimate the prevalence of SMA in the population using the life-table method.ResultsThis data analysis showed the presence of one copy of the SMN1 gene in 108 samples and two copies in 4090 samples, which resulted from a carrier frequency of 2.6%. The carrier frequency was twofold in females reaching 3.7% compared to 1.6% in males. 27% of participants were children of first-cousin marriages. We estimated the birth incidence of SMA to be 32 per 100,000 birth and the total number of people living with SMA in the Kingdom of Saudi Arabia to be 2265 of which 188 are type I, 1213 are type II, and 8,64 are type III.ConclusionThe SMA carrier rate of 2.6% in Saudi control subjects is slightly higher than the reported global frequency of 1.25 to 2% with links to the high degree of consanguinity.
| S-EPMC9651606 | biostudies-literature
Project description:BackgroundThis real-world data study analyzed glucose metrics from FreeStyle Libre® flash glucose monitoring in relation to scanning frequency, time in range (TIR) and estimated A1c (eA1c) in Saudi Arabia.MethodsAnonymized reader data were analyzed according to scanning frequency quartiles, eA1c categories (<7%,≥7%‒≤9% or>9%) and TIR categories (<50%,≥50%‒≤70% or>70%). Sensors, grouped by reader, were required to have≥120 h of operation. Differences in scanning frequency, eA1c, TIR, time in hypoglycemia and hyperglycemia, and glucose variability (standard deviation [SD] and coefficient of variation [CV]) were analyzed between groups.Results6097 readers, 35,747 sensors, and 40 million automatic glucose measurements were analyzed. Patients in the highest scanning frequency quartile (Q4, mean 32.0 scans/day) had lower eA1c (8.47%), greater TIR (46.4%) and lower glucose variation (SD 75.0 mg/dL, CV 38.2%) compared to the lowest quartile (Q1, mean 5.2 scans/day; eA1c 9.77%, TIR 32.8%, SD 94.9 mg/dL, CV 41.3%). Lower eA1c and higher TIR were associated with greater scanning frequency, lower glucose variability and less time in hyperglycemia.ConclusionsHigher scanning frequency in flash glucose users from Saudi Arabia is associated with lower eA1c, higher TIR, lower glucose variability and less time in hypoglycemia or hyperglycemia.
| S-EPMC9063302 | biostudies-literature
Project description:The COVID-19 pandemic damaged crude oil markets and amplified the consequences of uncertainty stemming from the Russia-Saudi Arabia oil price war in March-April of 2020. We investigate the impacts of the oil price war on global crude oil markets. By doing so, we use the daily futures and spot prices in three major crude oil markets - West Texas Intermediate, European Brent, and Oman - to perform a systematic analysis of the impacts of the oil price war on them. The event study method, a well-established analytical tool to measure the impacts of a given event on markets, is used in this study. The results indicate that information leakage plays an important role in the impacts of the price war. The outbreak of and truce following the price war have asymmetrical impacts on the markets; negative impacts generated by information leakage during the outbreak are generally more durable than the positive ones it generated during the truce. Furthermore, the magnitude of the impacts on futures markets is negatively correlated with the time-to-maturity of futures. Finally, negative crude oil prices affect West Texas Intermediate crude oil markets the most. Our findings generally show that market participants could perceive and assimilate market changes and adjust their expectations, which restrained the impacts that should have occurred within the oil price war.
| S-EPMC8652835 | biostudies-literature
Project description:BackgroundAfter recovery from acute infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), many patients experience long-term symptoms in different body systems. The aim of the present study was to identify these symptoms, their severity, and their duration as a first step in building a system to classify post-recovery long-term symptoms of coronavirus disease 2019 (COVID-19).MethodsAn online-based cross-sectional survey was administered between September and October 2020. Data regarding the severity of post-recovery symptoms and their duration were collected using an Arabic questionnaire divided into six categories encompassing the 20 most prevalent symptoms.ResultsA total of 979 patients recovered from COVID-19 in Saudi Arabia in the study period, of whom 53% were male and 47% were female. The most common symptoms included general fatigue and weakness (73% each), with moderate severity of neurological symptoms including mood changes (41%) and insomnia (39%). Among the special senses, loss of smell and taste of marked severity were reported by 64% and 55% among respiratory symptoms, cough of mild severity (47%), and dyspnea of moderate severity (43%). Loss of appetite of moderate severity was reported in 42%, and diarrhea, abdominal pain, and nausea of mild severity were reported by 53%, 50%, and 44% of respondents, respectively.ConclusionsLong-term symptoms after recovery from COVID-19 warrant patient follow-up. The authors propose a classification system as a starting point to guide the identification and follow-up of long-term symptoms post-recovery, and recommend larger-scale studies to broaden the definition of recovery from COVID-19, which appears to have two phases, acute and chronic.
| S-EPMC8654233 | biostudies-literature
Project description:AimTo minimize the spread of COVID-19, the Kingdom of Saudi Arabia (KSA) enforced a nationwide lockdown. We aimed to explore whether the manner in which Saudi patients with type 1 diabetes (T1D) manage their disease has changed during this unparalleled lockdown.MethodsAn online survey exploring the effect of lockdown on T1D outcomes was distributed among T1D patients residing in KSA during lockdown.ResultsA total of 1010 patients responded to the survey. Around 40% reported communicating with their physicians during lockdown. Age, level of education, residence, previous visits to diabetes education clinics, last HbA1c value, and average monthly income were all significantly associated with communication with the treating physician (p = 0.008, p < 0.001, p < 0.001, p = 0.002, p < 0.001, and p < 0.001, respectively). Age, level of education, and average monthly income were significantly associated with experiencing severe hypoglycemia (p = 0.036, p = 0.03, and p < 0.001, respectively), while average monthly income and level of education were significantly associated with experiencing diabetic ketoacidosis (DKA) (p < 0.001 and p = 0.0039, respectively); during lockdown. Patients who communicated with their physicians reported lower rates of severe hypoglycemia compared to those who did not (25.2% vs 30.7%, respectively).ConclusionAge and level of education were significantly associated with communication with the treating physician, and experiencing severe hypoglycemia and DKA; in patients with T1D during the lockdown period in Saudi Arabia. Keeping two-way virtual communication channels between physicians and their T1D patients should be encouraged.
| S-EPMC8282990 | biostudies-literature
Project description:The discovery of a new form of corona-viruses in December 2019, SARS-CoV-2, commonly named COVID-19, has reshaped the world. With health and economic issues at stake, scientists have been focusing on understanding the dynamics of the disease, in order to provide the governments with the best policies and strategies allowing them to reduce the span of the virus. The world has been waiting for the vaccine for more than one year. The World Health Organization (WHO) is advertising the vaccine as a safe and effective measure to fight off the virus. Saudi Arabia was the fourth country in the world to start to vaccinate its population. Even with the new simplified COVID-19 rules, the third dose is still mandatory. COVID-19 vaccines have raised many questions regarding in its efficiency and its role to reduce the number of infections. In this work, we try to answer these question and propose a new mathematical model with five compartments, including susceptible, vaccinated, infectious, asymptotic and recovered individuals. We provide theoretical results regarding the effective reproduction number, the stability of endemic equilibrium and disease free equilibrium. We provide numerical analysis of the model based on the Saudi case. Our developed model shows that the vaccine reduces the transmission rate and provides an explanation to the rise in the number of new infections immediately after the start of the vaccination campaign in Saudi Arabia.
| S-EPMC9137965 | biostudies-literature