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SARS-CoV-2 Genetic Variants and Patient Factors Associated with Hospitalization Risk

Korves et al., medRxiv, doi:10.1101/2024.03.08.24303818
Mar 2024  
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Retrospective 12,538 COVID-19 patients, showing associations between specific SARS-CoV-2 lineages and amino acid mutations and increased hospitalization risk, while infection with omicron was associated with lower hospitalization risk compared to prior variants. The study used machine learning (XGBoost) and hierarchical Bayesian modeling to analyze relationships between viral genomic features and hospitalization within 14 days, while accounting for patient risk factors, COVID-19 vaccination status, and monoclonal antibody treatment. Several lineages including B.1.1.7, AY.44, and AY.54 were associated with higher hospitalization risk. Amino acid changes in the spike protein N-terminal domain and in non-structural protein 14 were also associated with hospitalization risk.
Korves et al., 10 Mar 2024, USA, preprint, 5 authors. Contact:
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SARS-CoV-2 Genetic Variants and Patient Factors Associated with Hospitalization Risk
Tonia Korves, David Stein, David Walburger, Tomasz Adamusiak, Seth Roberts
Variants of SARS-CoV-2 have been associated with different transmissibilities and disease severities. The present study examines SARS-CoV-2 genetic variants and their relationship to risk for hospitalization, using data from 12,538 patients from a large, multisite observational cohort study. The association of viral genomic variants and hospitalization is examined with clinical covariates, including COVID-19 vaccination status, outpatient monoclonal antibody treatment status, and underlying risk for poor clinical outcome. Modeling approaches include XGBoost with SHapley Additive exPlanations (SHAP) analysis and generalized linear mixed models. The results indicate that several SARS-CoV-2 lineages are associated with increased hospitalization risk, including B.1.1.7, AY.44, and AY.54. As found in prior studies, Omicron is associated with lower hospitalization risk compared to prior WHO variants. In addition, the results suggest that variants at specific amino acid locations, including locations within Spike protein N-terminal domain and in non-structural protein 14, are associated with hospitalization risk.
Competing Interests There are no competing interests to declare.
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