2021
DOI: 10.1101/2021.12.21.21268116
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Early assessment of the clinical severity of the SARS-CoV-2 Omicron variant in South Africa

Abstract: Background 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 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. Methods We performed data linkages for (i) SARS-CoV-2 laboratory tests, (ii) COVID-19 case data, (iii) genome data, and (iv) the DATCOV … Show more

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Cited by 127 publications
(138 citation statements)
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“…However, infection with 8.18E+10 3 FFU in a 200 µL volume appeared to produce reduced clinical signs, delayed and reduced weight loss when compared to hamsters challenged with the ancestral virus, VIC01, at a comparable dose. This outcome appears to reflect the clinical description of human infection with this new variant of concern 44,45 . Despite these clear differences in clinical signs of infection in hamsters, shedding of virus in the upper respiratory tract was comparable for both the VIC01 and Omicron groups in the hamster model.…”
Section: Discussionsupporting
confidence: 59%
“…However, infection with 8.18E+10 3 FFU in a 200 µL volume appeared to produce reduced clinical signs, delayed and reduced weight loss when compared to hamsters challenged with the ancestral virus, VIC01, at a comparable dose. This outcome appears to reflect the clinical description of human infection with this new variant of concern 44,45 . Despite these clear differences in clinical signs of infection in hamsters, shedding of virus in the upper respiratory tract was comparable for both the VIC01 and Omicron groups in the hamster model.…”
Section: Discussionsupporting
confidence: 59%
“…The limited effect of Omicron's mutations on the T cell response suggests that vaccination or prior infection may still provide substantial protection from severe disease. Indeed, South Africa has reported a lower risk of hospitalisation and severe disease compared to the previous Delta wave 20 . Cross-reactive T cell responses acquired through vaccination or infection may contribute to these apparent milder outcomes for Omicron.…”
Section: Main Textmentioning
confidence: 99%
“…(https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/fil e/1043807/technical-briefing-33.pdf). In South Africa Omicron infections led to a lower incidence of severe disease relative to other variants 8 , although this can be at least partly explained by pre-existing immunity 1 . While Omicron infections are rising steeply, many countries still have high levels of infection with the Delta variant.…”
mentioning
confidence: 96%