ABSTRACT
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has demanded an unprecedented scientific response, with researchers collaborating on a global scale to better understand how host genetics can influence susceptibility to coronavirus infection and the severity of COVID-19 symptoms. The number of projects directed towards sequencing patients genomes has increased rapidly during this time with the rate of data generation outpacing the resources available for analysis and biological interpretation of these datasets. SNPnexus COVID is a cutting-edge web-based analytical platform that allows researchers to analyse and interpret the functional implications of genetic variants in COVID-19 patient genomes and to prioritise those that demonstrate clinical utility for the prevention, management and/or treatment of COVID-19. Our resource links to diverse multifactorial datasets and information resources that would require substantial time and computational power to otherwise mine independently. This streamlines biological data interpretation and allows researchers to better understand the multidimensional characteristics of their data. Importantly, SNPnexus COVID is powered by the SNPnexus software and follows its intuitive infrastructure, which precludes the need for programmatic experience in its users. SNPnexus COVID is freely available at https://www.snp-nexus.org/v4/covid/
ABSTRACT
ObjectiveTo explore risk factors associated with COVID-19 susceptibility and survival in patients with pre-existing hepato-pancreato-biliary (HPB) conditions. DesignCross-sectional study. SettingEast London Pancreatic Cancer Epidemiology (EL-PaC-Epidem) study at Barts Health NHS Trust, UK. Linked electronic health records were interrogated on a cohort of participants (age [≥] 18 years), reported with HPB conditions between 1 April 2008 and 6 March 2020. ParticipantsEL-PaC-Epidem study participants, alive on 12 February 2020, and living in East London within the previous six months (n=15 440). The cohort represents a multi-ethnic population with 51.7% belonging to the non-White background. Main outcome measureCOVID-19 incidence and mortality. ResultsSome 226 (1.5%) participants had confirmed COVID-19 diagnosis between 12 February and 12 June 2020, with an increased odds for men (OR 1.56; 95% CI 1.2 to 2.04) and Black ethnicity (2.04; 1.39 to 2.95) as well as patients with moderate to severe liver disease (2.2; 1.35 to 3.59). Each additional comorbidity increased the odds of infection by 62%. Substance mis-users were at more risk of infection, so were patients on Vitamin D treatment. The higher odds ratios in patients with chronic pancreatic or mild liver conditions, age>70, and history of smoking or obesity were due to co-existing comorbidities. Increased odds of death were observed for men (3.54; 1.68 to 7.85) and Black ethnicity (3.77; 1.38 to 10.7). Patients having respiratory complications from COVID-19 without a history of chronic respiratory disease also had higher odds of death (5.77; 1.75 to 19). ConclusionsIn this large population-based study of HPB patients, men, Black ethnicity, pre-existing moderate to severe liver conditions, six common medical multi-morbidities, substance mis-use, and a history of Vitamin D treatment independently posed higher odds of acquiring COVID-19 compared to their respective counterparts. The odds of death were significantly high for men and Black people. STRENGTHS AND LIMITATIONS OF THIS STUDYO_LIFirst multi-ethnic population-based study on COVID-19 in patients with hepato-pancreato-biliary group of diseases. C_LIO_LISystematic identification of the effect, or the lack of it, of individual demographic and clinical factors on the infection and mortality of COVID-19 in a large cohort of over 15 000 patients, robustly controlling for potential confounders in their evaluation. C_LIO_LIAccess to longitudinal data from linked primary and secondary care electronic health records, and use of rule-based phenotyping algorithms allowed for improved completeness and accuracy of the explored variables. C_LIO_LISome observed increased odds of SARS-CoV-2 infection and related death could be plausibly explained by unmeasured confounding. C_LIO_LIThe effects reported in the study could be influenced by the relatively smaller size of COVID-19 cases within this cohort. C_LI
