Circulating proteins to predict adverse COVID-19 outcomes (preprint)

Predicting COVID-19 severity is difficult, and the biological pathways involved are not fully understood. To approach this problem, we measured 4,701 circulating human protein abundances in two independent cohorts totaling 986 individuals. We then trained prediction models including protein abundances and clinical risk factors to predict adverse COVID-19 outcomes in 417 subjects and tested these models in a separate cohort of 569 individuals. For severe COVID-19, a baseline model including age and sex provided an area under the receiver operator curve (AUC) of 65% in the test cohort. Selecting 92 proteins from the 4,701 unique protein abundances improved the AUC to 88% in the training cohort, which remained relatively stable in the testing cohort at 86%, suggesting good generalizability. Proteins selected from different adverse COVID-19 outcomes were enriched for cytokine and cytokine receptors, but more than half of the enriched pathways were not immune-related. Taken together, these findings suggest that circulating proteins measured at early stages of disease progression are reasonably accurate predictors of adverse COVID-19 outcomes. Further research is needed to understand how to incorporate protein measurement into clinical care.

Circulating Proteins Influencing COVID-19 Susceptibility and Severity: a Mendelian Randomization Study (preprint)

Proteins detectable in peripheral blood may influence COVID-19 susceptibility or severity. However, understanding which circulating proteins are etiologically involved is difficult because their levels may be influenced by COVID-19 itself and also subject to confounding factors. To identify circulating proteins influencing COVID-19 susceptibility and severity we undertook a large-scale two-sample Mendelian randomization (MR) study, since this study design can rapidly scan hundreds of circulating proteins and reduces bias due to confounding and reverse causation. We began by identifying the genetic determinants of 955 circulating proteins in up to 10,708 SARS-CoV-2 uninfected individuals, retaining only single nucleotide polymorphisms near the gene encoded by the circulating protein. We then undertook an MR study to estimate the effect of these proteins on COVID-19 susceptibility and severity using the Host Genetics Initiative. We found that a standard deviation increase in OAS1 levels was associated with reduced COVID-19 death or ventilation (N = 2,972 cases / 284,472 controls; OR = 0.48, P = 7x10-8), COVID-19 hospitalization (N = 6,492 / 1,012,809; OR = 0.60, P = 2x10-7) and COVID-19 susceptibility (N = 17,607 / 1,345,334; OR = 0.81, P = 6x10-5). Results were consistent despite multiple sensitivity analyses probing MR assumptions. OAS1 is an interferon-stimulated gene that promotes viral RNA degradation. Other potentially implicated proteins included IL10RB. Available medicines, such as interferon-beta-1b, increase OAS1 and could be explored for their effect on COVID-19 susceptibility and severity.

Vitamin D and Covid-19 Susceptibility and Severity: a Mendelian Randomization Study (preprint)

Introduction Increased vitamin D levels, as reflected by 25OHD measurements, has been proposed to protect against Covid-19 disease based on in-vitro, observational, and ecological studies. However, vitamin D levels are associated with many confounding variables and thus associations described to date may not be causal. Vitamin D MR studies have provided results that are concordant with large-scale vitamin D randomized trials. Here, we used two-sample MR to assess the effect of circulating 25OHD levels on Covid-19 susceptibility. Methods Genetic variants strongly associated with 25OHD levels in a 443,734-participant genome-wide association study (GWAS) were used as instrumental variables. GWASs of Covid-19 susceptibility and severity from the Covid-19 Host Genetics Initiative were used to test the effect of 25OHD levels on these outcomes. Cohorts from the Covid-19 Host Genetics Initiative GWAS included up to 966,395 individuals of European ancestry. Results Genetically increased 25OHD levels by one standard deviation on the logarithmic scale had no clear effect on susceptibility but tended to increase the odds ratio of hospitalization (OR = 2.34; 95% CI: 1.33, 4.11) and severe disease (OR = 2.21; 95% CI: 0.87, 5.55). Extensive sensitivity analyses probing the assumptions of MR provided consistent estimates. Conclusion These findings do not support a protective role of increased 25OHD levels on Covid-19 outcomes and may suggest harm. At present, individuals should not use vitamin D supplements to protect against Covid-19 outcomes, and on-going supplementation trials should closely monitor for signals of harm.