Associations between SARS-CoV-2 variants and risk of COVID-19 hospitalization among confirmed cases in Washington State: a retrospective cohort study

Miguel I. Paredes, Stephanie M. Lunn, Michael Famulare, Lauren A. Frisbie, Ian Painter, Roy Burstein, Pavitra Roychoudhury, Hong Xie, Shah A. Mohamed Bakhash, Ricardo Perez, Maria Lukes, Sean Ellis, Saraswathi Sathees, Patrick C. Mathias, Alexander Greninger, Lea M. Starita, Chris D. Frazar, Erica Ryke, Weizhi Zhong, Luis Gamboa, Machiko Threlkeld, Jover Lee, Deborah A. Nickerson, Daniel L. Bates, Matthew E. Hartman, Eric Haugen, Truong N. Nguyen, Joshua D. Richards, Jacob L. Rodriguez, John A. Stamatoyannopoulos, Eric Thorland, Geoff Melly, Philip E. Dykema, Drew C. MacKellar, Hannah K. Gray, Avi Singh, JohnAric MoonDance Peterson, Denny Russell, Laura Marcela Torres, Scott Lindquist, Trevor Bedford, Krisandra J. Allen, Hanna N. Oltean

*These authors contributed equally to this work

Abstract

Background: The COVID-19 pandemic is now dominated by variant lineages; the resulting impact on disease severity remains unclear. Using a retrospective cohort study, we assessed the risk of hospitalization following infection with nine variants of concern or interest (VOC/VOI).

Methods: Our study includes individuals with positive SARS-CoV-2 RT-PCR in the Washington Disease Reporting System and with available viral genome data, from December 1, 2020 to July 30, 2021. The main analysis was restricted to cases with specimens collected through sentinel surveillance. Using a Cox proportional hazards model with mixed effects, we estimated hazard ratios (HR) for the risk of hospitalization following infection with a VOC/VOI, adjusting for age, sex, and vaccination status.

Findings: Of the 27,814 cases, 23,170 (83.3%) were sequenced through sentinel surveillance, of which 726 (3.1%) were hospitalized due to COVID-19. Higher hospitalization risk was found for infections with Gamma (HR 3.17, 95% CI 2.15-4.67), Beta (HR: 2.97, 95% CI 1.65–5.35), Delta (HR: 2.30, 95% CI 1.69-3.15), and Alpha (HR 1.59, 95% CI 1.26–1.99) compared to infections with an ancestral lineage. Following VOC infection, unvaccinated patients show a similar higher hospitalization risk, while vaccinated patients show no significant difference in risk, both when compared to unvaccinated, ancestral lineage cases.

Interpretation: Infection with a VOC results in a higher hospitalization risk, with an active vaccination attenuating that risk. Our findings support promoting hospital preparedness, vaccination, and robust genomic surveillance.

Organization

While data is not included due to patient privacy concerns, the code contained in this repository represent the analytic code for the above manuscript. If running with data from the Washington Department of Health, please begin by first running variant_severity_data_prep.R followed by variant_exploratory_descriptive_figures.R before continuing with the other analytic scripts.