Dataset Information

Omicron Subvariants: Clinical, Laboratory, and Cell Culture Characterization.

ABSTRACT:

Background

The variant of concern, Omicron, has become the sole circulating 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. In this study, we compare the clinical outcomes in patients infected with different Omicron subvariants and compare 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 to infections with BA.1. Cycle threshold values (Ct) and the recovery of infectious virus on VeroTMPRSS2 cell line from clinical specimens were compared.

Results

The BA.1 was associated with the largest increase in SARS-CoV-2 positivity rate and COVID-19 related hospitalizations at the Johns Hopkins system. After a peak in January cases fell 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 when compared to other Omicron subvariants. BA.5 samples had a greater likelihood of having infectious virus at Ct values less than 20.

Conclusions

Omicron subvariants continue to associate with a relatively high positivity and 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.

Funding

Centers for Disease Control and Prevention contract 75D30121C11061, NIH/NIAID Center of Excellence in Influenza Research and Surveillance contract HHS N2772201400007C, Johns Hopkins University, Maryland department of health, and The Modeling Infectious Diseases in Healthcare Network (MInD) under awards U01CK000589.

SUBMITTER: Morris CP

PROVIDER: S-EPMC9516865 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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Publications

Omicron Subvariants: Clinical, Laboratory, and Cell Culture Characterization.

Morris C Paul CP Eldesouki Raghda E RE Sachithanandham Jaiprasath J Fall Amary A Norton Julie M JM Abdullah Omar O Gallagher Nicholas N Li Maggie M Pekosz Andrew A Klein Eili Y EY Mostafa Heba H HH

medRxiv : the preprint server for health sciences 20220923

<h4>Background</h4>The variant of concern, Omicron, has become the sole circulating 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. In this study, we compare the clinical outcomes in patients infected with different Omicron subvariants and compare the relative viral loads, and recovery of infectious virus from upper respiratory spec ...[more]

PMID: 36172137

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Dataset Information

Omicron Subvariants: Clinical, Laboratory, and Cell Culture Characterization.

Background

Methods

Results

Conclusions

Funding

Publications

Omicron Subvariants: Clinical, Laboratory, and Cell Culture Characterization.

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