The displacement of the SARS-CoV-2 variant Delta with Omicron: An investigation of hospital admissions and upper respiratory viral loads
Amary Fall,
Raghda E. Eldesouki,
Jaiprasath Sachithanandham,
C. Paul Morris,
Julie M. Norton,
David C. Gaston,
Michael Forman,
Omar Abdullah,
Nicholas Gallagher,
Maggie Li,
Nicholas J. Swanson,
Andrew Pekosz,
Eili Y. Klein,
Heba H. Mostafa
Affiliations
Amary Fall
Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA
Raghda E. Eldesouki
Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA
Jaiprasath Sachithanandham
W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, USA
C. Paul Morris
Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA; National Institute of Allergy and Infectious Disease, National Institutes of Health, 615 North Wolfe Street, rm W2116, Bethesda, MD 20892, USA
Julie M. Norton
Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA
David C. Gaston
Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA
Michael Forman
Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA
Omar Abdullah
Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA
Nicholas Gallagher
Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA
Maggie Li
W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, USA
Nicholas J. Swanson
W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, USA
Andrew Pekosz
W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, USA; Department of Emergency Medicine, Johns Hopkins School of Medicine, 5801 Smith Ave, Davis Suite 3220, Baltimore, MD 21209, USA; Corresponding authors at: Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA.
Eili Y. Klein
Department of Emergency Medicine, Johns Hopkins School of Medicine, 5801 Smith Ave, Davis Suite 3220, Baltimore, MD 21209, USA; Center for Disease Dynamics, Economics, and Policy, Washington DC, USA; Corresponding authors at: Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA.
Heba H. Mostafa
Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA; Corresponding authors at: Department of Pathology, Division of Medical Microbiology, Johns Hopkins School of Medicine, Meyer B-121F, 600 N. Wolfe St, Baltimore, MD 21287, USA.
Summary: Background: The increase in SARS-CoV-2 infections in December 2021 was driven primarily by the Omicron variant, which largely displaced the Delta over a three-week span. Outcomes from infection with Omicron remain uncertain. We evaluated whether clinical outcomes and viral loads differed between Delta and Omicron infections during the period when both variants were co-circulating. Methods: In this retrospective observational cohort study, remnant clinical specimens, positive for SARS-CoV-2 after standard of care testing at the Johns Hopkins Microbiology Laboratory, between the last week of November and the end of December 2021, were used for whole viral genome sequencing. Cycle threshold values (Ct) for viral RNA, the presence of infectious virus, and levels of respiratory IgG were measured, and clinical outcomes were obtained. Differences in each measure were compared between variants stratified by vaccination status. Findings: The Omicron variant displaced Delta during the study period and constituted 95% of the circulating lineages by the end of December 2021. Patients with Omicron infections (N = 1,119) were more likely to be vaccinated compared to patients with Delta (N = 908), but were less likely to be admitted (0.33 CI 0.21–0.52), require ICU level care (0.38 CI 0.17–0.87), or succumb to infection (0.26 CI 0.06–1.02) regardless of vaccination status. There was no statistically significant difference in Ct values based on the lineage regardless of the vaccination status. Recovery of infectious virus in cell culture was reduced in boosted patients compared to fully vaccinated without a booster and unvaccinated when infected with the Delta lineage. However, in patients with Omicron infections, recovery of infectious virus was not affected by vaccination. Interpretation: Compared to Delta, Omicron was more likely to cause breakthrough infections of vaccinated individuals, yet admissions were less frequent. Admitted patients might develop severe disease comparable to Delta. Efforts for reducing Omicron transmission are required as, though the admission risk might be lower, the increased numbers of infections cause large numbers of hospitalizations. Funding: NIH/NIAID Center of Excellence in Influenza Research and Surveillance contract HHS N2772201400007C, Johns Hopkins University, Maryland department of health, Centers for Disease Control and Prevention contract 75D30121C11061, and The Modeling Infectious Diseases in Healthcare Network (MInD) under awards U01CK000589.
