@article{af523043502444adaed7acd5f27e8f74,
title = "Omicron Subvariants: Clinical, Laboratory, and Cell Culture Characterization",
abstract = "Background. The variant of concern Omicron has become the sole circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant for the past several months. Omicron subvariants BA.1, BA.2, BA.3, BA.4, and BA.5 evolved over the time, with BA.1 causing the largest wave of infections globally in December 2021–January 2022. This study compared the clinical outcomes in patients infected with different Omicron subvariants and the relative viral loads and recovery of infectious virus from upper respiratory specimens. Methods. SARS-CoV-2–positive remnant clinical specimens, diagnosed at the Johns Hopkins Microbiology Laboratory between December 2021 and July 2022, were used for whole-genome sequencing. The clinical outcomes of infections with Omicron subvariants were compared with infections with BA.1. Cycle threshold (Ct) values and the recovery of infectious virus on the VeroTMPRSS2 cell line from clinical specimens were compared. Results. BA.1 was associated with the largest increase in SARS-CoV-2 positivity rate and coronavirus disease 2019 (COVID-19)–related hospitalizations at the Johns Hopkins system. After a peak in January, cases decreased in the spring, but the emergence of BA.2.12.1 followed by BA.5 in May 2022 led to an increase in case positivity and admissions. BA.1 infections had a lower mean Ct value when compared with other Omicron subvariants. BA.5 samples had a greater likelihood of having infectious virus at Ct values <20. Conclusions. Omicron subvariants continue to be associated with a relatively high rate of polymerase chain reaction (PCR) positivity and hospital admissions. The BA.5 infections are more while BA.2 infections are less likely to have infectious virus, suggesting potential differences in infectibility during the Omicron waves.",
keywords = "Omicron, cell culture, cycle thresholds, live virus",
author = "Morris, {C. Paul} and Eldesouki, {Raghda E.} and Jaiprasath Sachithanandham and Amary Fall and Norton, {Julie M.} and Omar Abdullah and Nicholas Gallagher and Maggie Li and Andrew Pekosz and Klein, {Eili Y.} and Mostafa, {Heba H.}",
note = "Funding Information: This study was only possible with the unique efforts of the Johns Hopkins Clinical Microbiology Laboratory faculty and staff. This work was supported by the Centers for Disease Control and Prevention (CDC; contract number 75D30121C11061) (reported by H. H. M. and A. P.); the National Institutes of Health/National Institute of Allergy and Infectious Diseases (NIH/NIAID) Center of Excellence in Influenza Research and Surveillance Johns Hopkins Center of Excellence in Influenza Research and Surveillance (HHS N2772201400007C; reported by H. H. M. and A. P.); the National Institute on Drug Abuse, National Institute of Mental Health, and Office of AIDS Research of the NIH, the Department of Health and Human Services (UM1 AI068613); the NIH RADx-Tech program (3U54HL143541-02S2); the NIH RADx-UP initiative (grant number R01 DA045556-04S1); the Johns Hopkins University President{\textquoteright}s Fund Research Response; the Johns Hopkins Department of Pathology; and the Maryland Department of Health. H. H. M. is supported by the HIV Prevention Trials Network (HPTN) sponsored by NIAID. E. Y. K. was supported by the CDC Modeling Infectious Diseases in Healthcare Network (MInD)-Healthcare Program (grant number U01CK000589). H. H. M. reports grants or contracts from NIH UM1AI0686, NIH UM1 AI068613-14, NIH R01 DA045556-04S1, NIH 3U54HL143541-02S2, NIH 4UH3CA211396-03, and NIH R01 CA243393 and receipt of equipment, materials, drugs, medical writing, gifts or other services from BioRad (research contract), DiaSorin (research contract), and Hologic (research contract). R. E. E. reports a Pan American Society of Clinical Virology travel award. All other authors report no potential conflicts. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed. Funding Information: Potential conflicts of interest. H. H. M. reports grants or contracts from NIH UM1AI0686, NIH UM1 AI068613-14, NIH R01 DA045556-04S1, NIH 3U54HL143541-02S2, NIH 4UH3CA211396-03, and NIH R01 CA243393 and receipt of equipment, materials, drugs, medical writing, gifts or other services from BioRad (research contract), DiaSorin (research contract), and Hologic (research contract). R. E. E. reports a Pan American Society of Clinical Virology travel award. All other authors report no potential conflicts. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed. Publisher Copyright: {\textcopyright} The Author(s) 2022. Published by Oxford University Press on behalf of Infectious Diseases Society of America.",
year = "2023",
month = apr,
day = "1",
doi = "10.1093/cid/ciac885",
language = "English (US)",
volume = "76",
pages = "1276--1284",
journal = "Clinical Infectious Diseases",
issn = "1058-4838",
publisher = "Oxford University Press",
number = "7",
}