Disparities in COVID-19 infection, hospitalisation and death in people with schizophrenia, bipolar disorder, and major depressive disorder: a cohort study of the UK Biobank.

People with severe mental illness (SMI; including schizophrenia/psychosis, bipolar disorder (BD), major depressive disorder (MDD)) experience large disparities in physical health. Emerging evidence suggests this group experiences higher risks of infection and death from COVID-19, although the full extent of these disparities are not yet established. We investigated COVID-19 related infection, hospitalisation and mortality among people with SMI in the UK Biobank (UKB) cohort study. Overall, 447,296 participants from UKB (schizophrenia/psychosis = 1925, BD = 1483 and MDD = 41,448, non-SMI = 402,440) were linked with healthcare and death records. Multivariable logistic regression analysis was used to examine differences in COVID-19 outcomes by diagnosis, controlling for sociodemographic factors and comorbidities. In unadjusted analyses, higher odds of COVID-19 mortality were seen among people with schizophrenia/psychosis (odds ratio [OR] 4.84, 95% confidence interval [CI] 3.00-7.34), BD (OR 3.76, 95% CI 2.00-6.35), and MDD (OR 1.99, 95% CI 1.69-2.33) compared to people with no SMI. Higher odds of infection and hospitalisation were also seen across all SMI groups, particularly among people with schizophrenia/psychosis (OR 1.61, 95% CI 1.32-1.96; OR 3.47, 95% CI 2.47-4.72) and BD (OR 1.48, 95% CI 1.16-1.85; OR 3.31, 95% CI 2.22-4.73). In fully adjusted models, mortality and hospitalisation odds remained significantly higher among all SMI groups, though infection odds remained significantly higher only for MDD. People with schizophrenia/psychosis, BD and MDD have higher risks of COVID-19 infection, hospitalisation and mortality. Only a proportion of these disparities were accounted for by pre-existing demographic characteristics or comorbidities. Vaccination and preventive measures should be prioritised in these particularly vulnerable groups.

The need for integrated research autopsies in the era of precision oral medicine.

BACKGROUND: Autopsy has benefited the practice of medicine for centuries; however, its use to advance the practice of oral health care is relatively limited. In the era of precision oral medicine, the research autopsy is poised to play an important role in understanding oral-systemic health, including infectious disease, autoimmunity, craniofacial genetics, and cancer. TYPES OF STUDIES REVIEWED: The authors reviewed relevant articles that used medical and dental research autopsies to summarize the advantages of minimally invasive autopsies of dental, oral, and craniofacial tissues and to outline practices for supporting research autopsies of the oral and craniofacial complex. RESULTS: The authors provide a historical summary of research autopsy in dentistry and provide a perspective on the value of autopsies for high-resolution multiomic studies to benefit precision oral medicine. As the promise of high-resolution multiomics is being realized, there is a need to integrate the oral and craniofacial complex into the practice of autopsy in medicine. Furthermore, the collaboration of autopsy centers with researchers will accelerate the understanding of dental, oral, and craniofacial tissues as part of the whole body. CONCLUSIONS: Autopsies must integrate oral and craniofacial tissues as part of biobanking procedures. As new technologies allow for high-resolution, multimodal phenotyping of human samples, using optimized sampling procedures will allow for unprecedented understanding of common and rare dental, oral, and craniofacial diseases in the future. PRACTICAL IMPLICATIONS: The COVID-19 pandemic highlighted the oral cavity as a site for viral infection and transmission potential; this was only discovered via clinical autopsies. The realization of the integrated autopsy's value in full body health initiatives will benefit patients across the globe.

COVID-19 Mortality in the Colorado Center for Personalized Medicine Biobank.

Over 6.37 million people have died from COVID-19 worldwide, but factors influencing COVID-19-related mortality remain understudied. We aimed to describe and identify risk factors for COVID-19 mortality in the Colorado Center for Personalized Medicine (CCPM) Biobank using integrated data sources, including Electronic Health Records (EHRs). We calculated cause-specific mortality and case-fatality rates for COVID-19 and common pre-existing health conditions defined by diagnostic phecodes and encounters in EHRs. We performed multivariable logistic regression analyses of the association between each pre-existing condition and COVID-19 mortality. Of the 155,859 Biobank participants enrolled as of July 2022, 20,797 had been diagnosed with COVID-19. Of 5334 Biobank participants who had died, 190 were attributed to COVID-19. The case-fatality rate was 0.91% and the COVID-19 mortality rate was 122 per 100,000 persons. The odds of dying from COVID-19 were significantly increased among older men, and those with 14 of the 61 pre-existing conditions tested, including hypertensive chronic kidney disease (OR: 10.14, 95% CI: 5.48, 19.16) and type 2 diabetes with renal manifestations (OR: 5.59, 95% CI: 3.42, 8.97). Male patients who are older and have pre-existing kidney diseases may be at higher risk for death from COVID-19 and may require special care.

Combined effects of inflammation and coronavirus disease 2019 (COVID-19) on the risks of anxiety and depression: A cross-sectional study based on UK Biobank.

Infection-induced perturbation of immune homeostasis could promote psychopathology. Psychiatric sequelae have been observed after previous coronavirus outbreaks. However, limited studies were conducted to explore the potential interaction effects of inflammation and coronavirus disease 2019 (COVID-19) on the risks of anxiety and depression. In this study, first, polygenic risk scores (PRS) were calculated for eight COVID-19 clinical phenotypes using individual-level genotype data from the UK Biobank. Then, linear regression models were developed to assess the effects of COVID-19 PRS, C-reactive protein (CRP), systemic immune inflammation index (SII), and their interaction effects on the Generalized Anxiety Disorder-7 (GAD-7, 104 783 individuals) score and the Patient Health Questionnaire-9 (PHQ-9, 104 346 individuals) score. Several suggestive interactions between inflammation factors and COVID-19 clinical phenotypes were detected for PHQ-9 score, such as CRP/SII × Hospitalized/Not_Hospitalized in women group and CRP × Hospitalized/Unscreened in age >65 years group. For GAD-7 score, we also found several suggestive interactions, such as CRP × Positive/Unscreened in the age ≤65 years group. Our results suggest that not only COVID-19 and inflammation have important effects on anxiety and depression but also the interactions of COVID-19 and inflammation have serious risks for anxiety and depression.

Biobanking for COVID-19 research.

BACKGROUND: Biobanks are imperative infrastructures, particularly during outbreaks, when there is an obligation to acquire and share knowledge as quick as possible to allow for implementation of science-based preventive, diagnostic, prognostic, and therapeutic strategies. METHODS: We established a COVID-19 biobank with the aim of collecting high-quality and well-annotated human biospecimens, in the effort to understand the pathogenic mechanisms underlying COVID-19 and identify therapeutic targets (COVID-BioB, NCT04318366). Here we describe our experience and briefly review the characteristics of the biobanks for COVID-19 that have been so far established. RESULTS: A total of 46,677 samples have been collected from 913 participants (63.3% males, median [IQR] age 62.2 [51.2-74.0] years) since the beginning of the program. Most patients (66.9%) had been admitted to hospital for COVID-19, with a median length of stay of 15.0 (9.0-27.0) days. A minority of patients (13.3% of the total) had been admitted for other reasons and subsequently tested positive for SARS-CoV-2. The remainder were managed at home after being seen at the Emergency Department. CONCLUSIONS: Having a solid research infrastructure already in place, along with flexibility and adaptability to new requirements, allowed for the quick building of a COVID-19 biobank that will help expand and share the knowledge of SARS-CoV-2.

Association between blood N-3 fatty acid levels and the risk of coronavirus disease 2019 in the UK Biobank.

BACKGROUND: The role of nutritional status and the risk of contracting and/or experiencing adverse outcomes from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are unclear. Preliminary studies suggest that higher n-3 PUFA intakes are protective. OBJECTIVES: This study aimed to compare the risk of 3 coronavirus disease 2019 (COVID-19) outcomes (testing positive for SARS-CoV-2, hospitalization, and death) as a function of the baseline plasma DHA levels. METHODS: The DHA levels (% of total fatty acids [FAs]) were measured by nuclear magnetic resonance. The 3 outcomes and relevant covariates were available for 110,584 subjects (hospitalization and death) and for 26,595 ever-tested subjects (positive for SARS-CoV-2) in the UK Biobank prospective cohort study. Outcome data between 1 January, 2020, and 23 March, 2021, were included. The Omega-3 Index (O3I) (RBC EPA + DHA%) values across DHA% quintiles were estimated. The multivariable Cox proportional hazards models were constructed, and linear (per 1 SD) relations with the risk of each outcome were computed as HRs. RESULTS: In the fully adjusted models, comparing the fifth to the first DHA% quintiles, the HRs (95% confidence intervals) for testing positive, being hospitalized, and dying with COVID-19 were 0.79 (0.71, 0.89, P < 0.001), 0.74 (0.58, 0.94, P < 0.05), and 1.04 (0.69-1.57, not significant), respectively. On a per 1-SD increase in DHA% basis, the HRs for testing positive, hospitalization, and death, were 0.92 (0.89, 0.96, P < 0.001), 0.89 (0.83, 0.97, P < 0.01), and 0.95 (0.83, 1.09), respectively. The estimated O3I values across DHA quintiles ranged from 3.5% (quintile 1) to 8% (quintile 5). CONCLUSIONS: These findings suggest that nutritional strategies to increase the circulating n-3 PUFA levels, such as increased consumption of oily fish and/or use of n-3 FA supplements, may reduce the risk of adverse COVID-19 outcomes.

Effect of replacing television viewing with different intensities of physical activity on COVID-19 mortality risk: Short communication from UK Biobank.

AIMS: This study aimed to examine the theoretical effects of replacing television (TV) viewing with different intensities of physical activity on COVID-19 mortality risk using isotemporal substitution models. METHODS: The analytical sample was composed of 359,756 UK Biobank participants. TV viewing and physical activity were assessed by self-report. Logistic regressions adjusted for covariates were used to model the effects of substituting an hour a day of TV viewing with an hour of walking, moderate-intensity physical activity (MPA) or vigorous-intensity physical activity (VPA) on COVID-19 mortality risk. RESULTS: From 16 March 2020 to 12 November 2021, there were 879 COVID-19 deaths in the analytical sample. Substituting an hour a day of TV viewing with an hour of walking was associated with a 17% lower risk of COVID-19 mortality (odds ratio (OR)=0.83, 95% confidence interval (CI) 0.74-0.92). In sex-stratified analyses, the same substitution was associated with a lower risk in both men (OR=0.85, 95% CI 0.74-0.96) and women (OR=0.78, 95% CI 0.65-0.95). However, replacing an hour a day of TV viewing with an hour of MPA was only associated with a lower risk in women (OR=0.80, 95% CI 0.65-0.98). CONCLUSIONS: Replacing TV viewing with walking was associated with a significant reduction in COVID-19 mortality risk. Public health authorities should consider promoting the replacement of TV viewing with walking as a protective strategy against COVID-19 mortality.

Cohort profile: A Québec-based plasma donor biobank to study COVID-19 immunity (PlasCoV).

PURPOSE: The long-term humoral immunity to COVID-19 is not well understood owing to the continuous emergence of new variants of concern, the evolving vaccine-induced and infection-induced immunity, and the limited duration of follow-up in previous studies. As the sole blood service in Québec (Canada), Héma-Québec established a COVID-19-focused biobank ('PlasCoV') in April 2021. PARTICIPANTS: As of January 2022, the biobank included 86 483 plasma samples from 15 502 regular donors (age range=18-84 years, females=49.7%), for an average of 5.6 donations per donor. Nearly two-thirds (65.6%) of biobank donors made at least two donations, with many donors having provided samples prevaccination and postvaccination (3061 (19.7%)) or preinfection and postinfection (131 (0.8%)), thus allowing for longitudinal studies on vaccine-induced and infection-induced immunity. FINDINGS TO DATE: A study that used PlasCoV samples revealed that previously infected individuals who received a single dose of the BNT162b2 COVID-19 vaccine exhibited the strongest immune response. By contrast, SARS-CoV-2-naïve individuals required two vaccine doses to produce a maximal immune response. Furthermore, the results of a four-phase seroprevalence study indicated that the antinucleocapsid (N) response wanes rapidly, so that up to one-third of previously infected donors were seronegative for anti-N. FUTURE PLANS: Donations from individuals who consented to participate before 1 October 2022 will be collected up until 31 March 2023. This plasma biobank will facilitate the conduct of longitudinal studies on COVID-19 immunity, thus helping to provide valuable insights into the anti-SARS-CoV-2 immune response and its persistence, and the effects of vaccination and variants on the specificity of the anti-SARS-CoV-2 immune response.

New Horizons: the value of UK Biobank to research on endocrine and metabolic disorders.

UK Biobank is an intensively characterized prospective study of 500 000 men and women, aged 40 to 69 years when recruited, between 2006 and 2010, from the general population of the United Kingdom. Established as an open-access resource for researchers worldwide to perform health research that is in the public interest, UK Biobank has collected (and continues to collect) a vast amount of data on genetic, physiological, lifestyle, and environmental factors, with prolonged follow-up of heath conditions through linkage to administrative electronic health records. The study has already demonstrated its unique value in enabling research into the determinants of common endocrine and metabolic diseases. The importance of UK Biobank, heralded as a flagship project for UK health research, will only increase over time as the number of incident disease events accrue, and the study is enhanced with additional data from blood assays (such as whole-genome sequencing, metabolomics, and proteomics), wearable technologies (including physical activity and cardiac monitors), and body imaging (magnetic resonance imaging and dual-energy X-ray absorptiometry). This unique research resource is likely to transform our understanding of the causes, diagnosis, and treatment of many endocrine and metabolic disorders.

Associations of socioeconomic status with infectious diseases mediated by lifestyle, environmental pollution and chronic comorbidities: a comprehensive evaluation based on UK Biobank.

BACKGROUND: Socioeconomic status (SES) inequity was recognized as a driver of some certain infectious diseases. However, few studies evaluated the association between SES and the burden of overall infections, and even fewer identified preventable mediators. This study aimed to assess the association between SES and overall infectious diseases burden, and the potential roles of factors including lifestyle, environmental pollution, chronic disease history. METHODS: We included 401,009 participants from the UK Biobank (UKB) and defined the infection status for each participant according to their diagnosis records. Latent class analysis (LCA) was used to define SES for each participant. We further defined healthy lifestyle score, environment pollution score (EPS) and four types of chronic comorbidities. We used multivariate logistic regression to test the associations between the four above covariates and infectious diseases. Then, we performed the mediation and interaction analysis to explain the relationships between SES and other variables on infectious diseases. Finally, we employed seven types of sensitivity analyses, including considering the Townsend deprivation index as an area level SES variable, repeating our main analysis for some individual or composite factors and in some subgroups, as well as in an external data from the US National Health and Nutrition Examination Survey, to verify the main results. RESULTS: In UKB, 60,771 (15.2%) participants were diagnosed with infectious diseases during follow-up. Lower SES [odds ratio (OR) = 1.5570] were associated with higher risk of overall infections. Lifestyle score mediated 2.9% of effects from SES, which ranged from 2.9 to 4.0% in different infection subtypes, while cardiovascular disease (CVD) mediated a proportion of 6.2% with a range from 2.1 to 6.8%. In addition, SES showed significant negative interaction with lifestyle score (OR = 0.8650) and a history of cancer (OR = 0.9096), while a significant synergy interaction was observed between SES and EPS (OR = 1.0024). In subgroup analysis, we found that males and African (AFR) with lower SES showed much higher infection risk. Results from sensitivity and validation analyses showed relative consistent with the main analysis. CONCLUSIONS: Low SES is shown to be an important risk factor for infectious disease, part of which may be mediated by poor lifestyle and chronic comorbidities. Efforts to enhance health education and improve the quality of living environment may help reduce burden of infectious disease, especially for people with low SES.

Diet-Related Inflammation Is Associated with Worse COVID-19 Outcomes in the UK Biobank Cohort.

Diet, the most important modulator of inflammatory and immune responses, may affect COVID-19 incidence and disease severity. Data from 196,154 members of the UK biobank had at least one 24 h dietary recall. COVID-19 outcomes were based on PCR testing, hospital admissions, and death certificates. Adjusted Poisson regression analyses were performed to estimate the risk ratios (RR) and their 95% confidence intervals (CI) for dietary inflammatory index (DII)/energy-adjusted DII (E-DII) scores. Models were adjusted for sociodemographic factors, comorbidities, smoking status, physical activity, and sleep duration. Between January 2020 and March 2021, there were 11,288 incident COVID-19 cases, 1270 COVID-19-related hospitalizations, and 315 COVID-19-related deaths. The fully adjusted model showed that participants in the highest (vs. lowest) DII/E-DII quintile were at 10-17% increased risk of COVID-19 (DII: RR Q5 vs. Q1 = 1.10, 95% CI 1.04-1.17, Ptrend < 0.001; E-DII: RR Q5 vs. Q1 = 1.17, 95% CI 1.10-1.24, Ptrend < 0.001) and ≈40% higher risk was observed for disease severity (DII: RR Q5 vs. Q1 = 1.40, 95% CI 1.18-1.67, Ptrend < 0.001; E-DII: RR Q5 vs. Q1 = 1.39, 95% CI 1.16-1.66, Ptrend < 0.001). There was a 43% increased risk of COVID-19-related death in the highest DII quintile (RR Q5 vs. Q1 = 1.43, 95% CI 1.01-2.01, Ptrend = 0.04). About one-quarter of the observed positive associations between DII and COVID-19-related outcomes were mediated by body mass index (25.8% for incidence, 21.6% for severity, and 19.8% for death). Diet-associated inflammation increased the risk of COVID-19 infection, severe disease, and death.

Deep learning identified genetic variants for COVID-19-related mortality among 28,097 affected cases in UK Biobank.

Analysis of host genetic components provides insights into the susceptibility and response to viral infection such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19). To reveal genetic determinants of susceptibility to COVID-19 related mortality, we train a deep learning model to identify groups of genetic variants and their interactions that contribute to the COVID-19 related mortality risk using the UK Biobank data (28,097 affected cases and 1656 deaths). We refer to such groups of variants as super variants. We identify 15 super variants with various levels of significance as susceptibility loci for COVID-19 mortality. Specifically, we identify a super variant (odds ratio [OR] = 1.594, p = 5.47 × 10-9 ) on Chromosome 7 that consists of the minor allele of rs76398985, rs6943608, rs2052130, 7:150989011_CT_C, rs118033050, and rs12540488. We also discover a super variant (OR = 1.353, p = 2.87 × 10-8 ) on Chromosome 5 that contains rs12517344, rs72733036, rs190052994, rs34723029, rs72734818, 5:9305797_GTA_G, and rs180899355.

Laboratory diagnosed microbial infection in English UK Biobank participants in comparison to the general population.

Understanding the genetic and environmental risk factors for serious bacterial infections in ageing populations remains incomplete. Utilising the UK Biobank (UKB), a prospective cohort study of 500,000 adults aged 40-69 years at recruitment (2006-2010), can help address this. Partial implementation of such a system helped groups around the world make rapid progress understanding risk factors for SARS-CoV-2 infection and COVID-19, with insights appearing as early as May 2020. In principle, such approaches could also to be used for bacterial isolations. Here we report feasibility testing of linking an England-wide dataset of microbial reporting to UKB participants, to enable characterisation of microbial infections within the UKB Cohort. These records pertain mainly to bacterial isolations; SARS-CoV-2 isolations were not included. Microbiological infections occurring in patients in England, as recorded in the Public Health England second generation surveillance system (SGSS), were linked to UKB participants using pseudonymised identifiers. By January 2015, ascertainment of laboratory reports from UKB participants by SGSS was estimated at 98%. 4.5% of English UKB participants had a positive microbiological isolate in 2015. Half of UKB isolates came from 12 laboratories, and 70% from 21 laboratories. Incidence rate ratios for microbial isolation, which is indicative of serious infection, from the UKB cohort relative to the comparably aged general population ranged from 0.6 to 1, compatible with the previously described healthy participant bias in UKB. Data on microbial isolations can be linked to UKB participants from January 2015 onwards. This linked data would offer new opportunities for research into the role of bacterial agents on health and disease in middle to-old age.

Trends in incident diagnoses and drug prescriptions for anxiety and depression during the COVID-19 pandemic: an 18-month follow-up study based on the UK Biobank.

Serious concerns have been raised about the negative effects of the COVID-19 pandemic on population psychological well-being. However, limited data exist on the long-term effects of the pandemic on incident psychiatric morbidities among individuals with varying exposure to the pandemic. Leveraging prospective data from the community-based UK Biobank cohort, we included 308,400 participants free of diagnosis of anxiety or depression, as well as 213,757 participants free of anxiolytics or antidepressants prescriptions, to explore the trends in incident diagnoses and drug prescriptions for anxiety and depression from 16 March 2020 to 31 August 2021, compared to the pre-pandemic period (i.e., 1 January 2017 to 31 December 2019) and across populations with different exposure statuses (i.e., not tested for COVID-19, tested negative and tested positive). The age- and sex-standardized incidence ratios (SIRs) were calculated by month which indicated an increase in incident diagnoses of anxiety or depression among individuals who were tested for COVID-19 (tested negative: SIR 3.05 [95% confidence interval 2.88-3.22]; tested positive: 2.03 [1.76-2.34]), especially during the first six months of the pandemic (i.e., March-September 2020). Similar increases were also observed for incident prescriptions of anxiolytics or antidepressants (tested negative: 1.56 [1.47-1.67]; tested positive: 1.41 [1.22-1.62]). In contrast, individuals not tested for COVID-19 had consistently lower incidence rates of both diagnoses of anxiety or depression (0.70 [0.67-0.72]) and prescriptions of respective psychotropic medications (0.70 [0.68-0.72]) during the pandemic period. These data suggest a distinct rise in health care needs for anxiety and depression among individuals tested for COVID-19, regardless of the test result, in contrast to a reduction in health care consumption for these disorders among individuals not tested for and, presumably, not directly exposed to the disease.

High grip strength attenuates risk of severe COVID-19 in males but not females with obesity: A short communication of prospective findings from UK Biobank.

We examined the joint associations of BMI category and grip strength tertile with risk of severe COVID-19 (inpatient COVID-19 or COVID-19 mortality) in 327 500 UK Biobank participants. Compared to normal-weight males with high grip strength, the odds ratio (95 % confidence interval) for males with obesity with low grip strength was 2.39 (1.59-3.60), but 1.52 (0.98-2.35) for males with obesity with a high grip strength. A higher grip strength did not appear to be associated with lower risk of severe COVID-19 in females. Muscle mass and strength development should be considered as a means to reduce risk of severe COVID-19 for males with obesity.

Virus exposure and neurodegenerative disease risk across national biobanks.

With recent findings connecting the Epstein-Barr virus to an increased risk of multiple sclerosis and growing concerns regarding the neurological impact of the coronavirus pandemic, we examined potential links between viral exposures and neurodegenerative disease risk. Using time series data from FinnGen for discovery and cross-sectional data from the UK Biobank for replication, we identified 45 viral exposures significantly associated with increased risk of neurodegenerative disease and replicated 22 of these associations. The largest effect association was between viral encephalitis exposure and Alzheimer's disease. Influenza with pneumonia was significantly associated with five of the six neurodegenerative diseases studied. We also replicated the Epstein-Barr/multiple sclerosis association. Some of these exposures were associated with an increased risk of neurodegeneration up to 15 years after infection. As vaccines are currently available for some of the associated viruses, vaccination may be a way to reduce some risk of neurodegenerative disease.

Establishing the First COVID-19 Convalescent Plasma Biobank in Jordan.

Background: Antibodies with the specialized ability to fight infection can be found in the blood of individuals who have recovered from or have been vaccinated against COVID-19. As a result, plasma from these individuals could be used to treat critically ill patients. This treatment is known as convalescent plasma (CCP) therapy. Methods: Plasma units from 1555 consented healthy blood bank donors were collected from February to September 2021. Blood units were tested for the quantitative determination of Immunoglobulin G (IgG) antibodies to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus using one of the following assays based on the availability of the kits: The LIAISON® SARS-CoV-2 TrimericS IgG assay or the Abbott SARS-CoV-2 IgG II Quant assay. Results: Among the tested donors, 1027 participants tested positive for neutralizing anti-SARS-CoV-2 IgG antibodies (66.04%). There were 484 donors whose plasma qualified to be used for CCP therapy (47.13%) and 214 CCP units were stored in the COVID-19 convalescent biobank. Conclusion: We were able to identify and store 214 fresh frozen plasma units qualified for CCP-plasma therapy for COVID-19 patients according to World Health Organization standards. Hence, we established the first COVID-19-convalescent plasma data and plasma biobank for treating COVID-19-infected cancer patients in Jordan and the region.

Association of COVID-19 with short- and long-term risk of cardiovascular disease and mortality: a prospective cohort in UK Biobank.

AIMS: This study aims to evaluate the short- and long-term associations between COVID-19 and development of cardiovascular disease (CVD) outcomes and mortality in the general population. METHODS AND RESULTS: A prospective cohort of patients with COVID-19 infection between 16 March 2020 and 30 November 2020 was identified from UK Biobank, and followed for up to 18 months, until 31 August 2021. Based on age (within 5 years) and sex, each case was randomly matched with up to 10 participants without COVID-19 infection from two cohorts-a contemporary cohort between 16 March 2020 and 30 November 2020 and a historical cohort between 16 March 2018 and 30 November 2018. The characteristics between groups were further adjusted with propensity score-based marginal mean weighting through stratification. To determine the association of COVID-19 with CVD and mortality within 21 days of diagnosis (acute phase) and after this period (post-acute phase), Cox regression was employed. In the acute phase, patients with COVID-19 (n = 7584) were associated with a significantly higher short-term risk of CVD {hazard ratio (HR): 4.3 [95% confidence interval (CI): 2.6- 6.9]; HR: 5.0 (95% CI: 3.0-8.1)} and all-cause mortality [HR: 81.1 (95% CI: 58.5-112.4); HR: 67.5 (95% CI: 49.9-91.1)] than the contemporary (n = 75 790) and historical controls (n = 75 774), respectively. Regarding the post-acute phase, patients with COVID-19 (n = 7139) persisted with a significantly higher risk of CVD in the long-term [HR: 1.4 (95% CI: 1.2-1.8); HR: 1.3 (95% CI: 1.1- 1.6)] and all-cause mortality [HR: 5.0 (95% CI: 4.3-5.8); HR: 4.5 (95% CI: 3.9-5.2) compared to the contemporary (n = 71 296) and historical controls (n = 71 314), respectively. CONCLUSIONS: COVID-19 infection, including long-COVID, is associated with increased short- and long-term risks of CVD and mortality. Ongoing monitoring of signs and symptoms of developing these cardiovascular complications post diagnosis and up till at least a year post recovery may benefit infected patients, especially those with severe disease.

BIGwas: Single-command quality control and association testing for multi-cohort and biobank-scale GWAS/PheWAS data.

BACKGROUND: Genome-wide association studies (GWAS) and phenome-wide association studies (PheWAS) involving 1 million GWAS samples from dozens of population-based biobanks present a considerable computational challenge and are carried out by large scientific groups under great expenditure of time and personnel. Automating these processes requires highly efficient and scalable methods and software, but so far there is no workflow solution to easily process 1 million GWAS samples. RESULTS: Here we present BIGwas, a portable, fully automated quality control and association testing pipeline for large-scale binary and quantitative trait GWAS data provided by biobank resources. By using Nextflow workflow and Singularity software container technology, BIGwas performs resource-efficient and reproducible analyses on a local computer or any high-performance compute (HPC) system with just 1 command, with no need to manually install a software execution environment or various software packages. For a single-command GWAS analysis with 974,818 individuals and 92 million genetic markers, BIGwas takes ∼16 days on a small HPC system with only 7 compute nodes to perform a complete GWAS QC and association analysis protocol. Our dynamic parallelization approach enables shorter runtimes for large HPCs. CONCLUSIONS: Researchers without extensive bioinformatics knowledge and with few computer resources can use BIGwas to perform multi-cohort GWAS with 1 million GWAS samples and, if desired, use it to build their own (genome-wide) PheWAS resource. BIGwas is freely available for download from http://github.com/ikmb/gwas-qc and http://github.com/ikmb/gwas-assoc.