Predicting COVID-19 hospitalisation and common disease risk from comorbid diagnoses in 13 million individuals

Predicting disease risk from prior diagnoses is fundamental to clinical decision-making, particularly during health emergencies such as the COVID-19 pandemic, when individuals with long-term conditions may be disproportionately vulnerable to adverse outcomes. Despite intense interest in developing models to predict disease risk from prior diagnoses (1-3), most prediction models do not estimate effects of each prior diagnosis on disease risk conditional on other diagnoses, limiting interpretability and clinical utility. We developed the Comorbidity Risk Score (CRS), trained on 13 million individuals (age 40-69) from linked electronic health record (EHR) datasets of the entire population of England, to predict COVID-19 hospitalisation and 87 other disease outcomes. CRS was trained at close to saturated sample size and precisely estimated the effects of 212 prior diagnoses on the 88 disease outcomes, conditional on all other prior diagnoses. Correlations of CRS effect sizes across outcomes (e.g. 0.76 for myocardial infarction vs. hyperlipidaemia) matched the corresponding genetic correlations (e.g. 0.79 for myocardial infarction vs. hyperlipidaemia), confirming that comorbidity architectures capture disease aetiology. On average, CRS identified 5% of the population with 3.4-fold higher disease risk, including myocardial infarction (4.4-fold), lung cancer (6.5-fold), and COVID-19 hospitalisation (6.3-fold). Using prior diagnoses alone, CRS outperformed state-of-the-art clinical COVID-19 models (4). Furthermore, CRS (N=13 million) substantially outperformed state-of-the-art AI (1) (N=0.5 million) and linear (3) (N=0.5 million) models in predicting disease risk, suggesting that training sample size outweighs model complexity. CRS attained near-perfect transferability across self-reported ethnicities (e.g., Black vs. White: AUROC ratio = 97.3%). Finally, CRS distinguished independently predictive comorbidities from indirect associations, e.g., lipid metabolism disorder was a strong predictor of myocardial infarction risk but not ischaemic stroke, after conditioning on other prior diagnoses. In conclusion, CRS provides a comprehensive resource for understanding the impact of comorbidities on COVID-19 and other future diseases, revealing disease aetiology while enabling powerful prediction of disease risk.