Contrasting factors associated with COVID-19-related ICU and death outcomes: interpretable multivariable analyses of the UK CHESS dataset. (preprint)

BackgroundIdentifying factors associated with severe COVID-19 is a priority to guide clinical care and resource use in this pandemic. MethodsThis cohort comprised 13954 in-patients with confirmed COVID-19. Study outcomes were death and intensive care unit admission (ICUA). Multivariable logistic regression estimated odd ratios adjusted for 37 covariates (comorbidities, demographic, and others). Gradient boosted decision tree (GBDT) classification generated Shapley values evaluating the impact of covariates for each patient. FindingsDeaths due to COVID-19 were associated with immunosuppression due to disease (Odds Ratio 1.39, 95%CI [1.10-1.76]), type-2 diabetes (1.31, [1.17-1.46]), chronic respiratory disease (1.19, [1.05-1.35]), obesity (1.16, [1.01-1.33], age (1.56/10-year increment, [1.52-1.61]), and male sex (1.54, [1.42-1.68]). Associations with ICUA differed in direction (e.g., age, chronic respiratory disease) and in scale, e.g., obesity (3.37, [2.90-3.92]) for some factors. Ethnicity was strongly but variably associated with both outcomes, for example Irish ethnicity is negatively with death but not ICUA. GBDTs had similar performance (ROC-AUC, ICUA 0.83, death 0.68 for GBDT; 0.80 and 0.68 for logistic regression). Shapley explanations overall were consistent with odds ratios. Chronic heart disease, hypertension, other comorbidities, and some ethnicities had Shapley impacts on death ranging from positive to negative among different patients, although consistently associated with ICUA for all. Immunosuppressive disease, type-2 diabetes, and chronic liver and respiratory diseases had positive impacts on death with either positive or negative on ICUA. InterpretationVery different association of some factors, e.g., obesity, with death and ICUA may guide review of practice. Shapley explanation identified varying effects among patients emphasising the importance of individual patient assessment.

The Invasive Respiratory Infection Surveillance (IRIS) Initiative reveals significant reductions in invasive bacterial infections during the COVID-19 pandemic (preprint)

BackgroundStreptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis are leading causes of invasive diseases including bacteraemic pneumonia and meningitis, and of secondary infections post-viral respiratory disease. They are typically transmitted via respiratory droplets. We investigated rates of invasive disease due to these pathogens during the early phase of the COVID-19 pandemic. MethodsLaboratories in 26 countries across six continents submitted data on cases of invasive disease due to S pneumoniae, H influenzae and N meningitidis from 1 January 2018 to 31 May 2020. Weekly cases in 2020 vs 2018-2019 were compared. Streptococcus agalactiae data were collected from nine laboratories for comparison to a non-respiratory pathogen. The stringency of COVID-19 containment measures was quantified by the Oxford COVID-19 Government Response Tracker. Changes in population movements were assessed by Google COVID-19 Community Mobility Reports. Interrupted time series modelling quantified changes in rates of invasive disease in 2020 relative to when containment measures were imposed. FindingsAll countries experienced a significant, sustained reduction in invasive diseases due to S pneumoniae, H influenzae and N meningitidis, but not S agalactiae, in early 2020, which coincided with the introduction of COVID-19 containment measures in each country. Similar impacts were observed across most countries despite differing stringency in COVID-19 control policies. There was no evidence of a specific effect due to enforced school closures. InterpretationThe introduction of COVID-19 containment policies and public information campaigns likely reduced transmission of these bacterial respiratory pathogens, leading to a significant reduction in life-threatening invasive diseases in many countries worldwide.