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Early assessment of the clinical severity of the SARS-CoV-2 Omicron variant in South Africa

The SARS-CoV-2 Omicron variant of concern (VOC) almost completely replaced other variants in South Africa during November 2021 and was associated with a rapid increase in COVID-19 cases. We aimed to assess the clinical severity of individuals infected with Omicron, using S Gene Target Failure (SGTF) on the Thermo Fisher Scientific TaqPath COVID-19 PCR test as a proxy.

Early analyses suggest a reduced risk of hospitalization among SGTF-infected individuals when compared to non-SGTF infected individuals in the same time period. Once hospitalized, the risk of severe disease was similar for SGTF- and non-SGTF infected individuals, while SGTF-infected individuals had a reduced risk of severe disease when compared to earlier Delta-infected individuals. Some of this reduction is likely a result of high population immunity.

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