Andrew Boulle and colleagues at the Western Cape Government Health Department and the University of Cape Town in South Africa will use a data science approach applied to anonymised COVID-19 health data from the government health department including over one million tests and 60,000 hospital admissions, to study the clinical epidemiology and evolution of a new variant of SARS-CoV-2 that emerged in South Africa and the impact on patients with existing health conditions. They will conduct a case-control study to determine the clinical severity of the variant and use a cross-sectional design to explore the evolution of viral load. They will also analyse the impact of COVID-19 on pregnancy by evaluating birth weight and other birth outcomes, such as still births, and use death registries to determine mortality rates in patients with HIV, TB, and diabetes.
Publications
| Title | Journal | Date |
Driver Project | Abstract |
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| medRXiv | Oct 22 | DP-ACCORD | Mortality occurred in 5.7% (95% CI: 5.3,6.0) of 17 831 first diagnosed infections. Higher mortality was associated with lower recent CD4, no evidence of ART collection, high or unknown recent viral load (among those with ART evidence), and recent first HIV evidence, differentially by age… | |
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medRXiv | Jul 2022 | DP – ACCORD | We aimed to compare clinical severity of Omicron BA.4/BA.5 infection with BA.1 and earlier variant infections among laboratory-confirmed SARS-CoV-2 cases in the Western Cape, South Africa, using timing of infection to infer the lineage/variant causing infection… |
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Wiley online library |
June 2022 | DP – ACCORD | The objective was to compare COVID-19 outcomes in the Omicron-driven fourth wave with prior waves in the Western Cape, assess the contribution of undiagnosed prior infection to differences in outcomes in a context of high seroprevalence due to prior infection and determine whether protection against severe disease conferred by prior infection and/or vaccination was maintained… | |
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International Journal of Infectious Diseases |
May 2022 | DP-ACCORD | At present, it is unclear whether the extent of reduced risk of severe disease seen with SARS-Cov-2 Omicron variant infection is caused by a decrease in variant virulence or by higher levels of population immunity… |
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Journal of Virological Methods |
Jan 2022 | DP-ACCORD | Routine SARS-CoV-2 surveillance in the Western Cape region of South Africa (January-August 2021) found a reduced RT-PCR amplification efficiency of the RdRp-gene target of the Seegene, Allplex 2019-nCoV diagnostic assay from June 2021 when detecting the Delta variant… | |
| medRXiv | Jan 2022 | DP-ACCORD | We aimed to compare COVID-19 outcomes in the Omicron-driven fourth wave with prior waves in the Western Cape, the contribution of undiagnosed prior infection to differences in outcomes in a context of high seroprevalence due to prior infection, and whether protection against severe disease conferred by prior infection and/or vaccination was maintained. | |
| medRXiv | Jan 2022 | DP-ACCORD | Emerging data suggest that SARS-CoV-2 Omicron variant of concern (VOC)is associated with reduced risk of severe disease. The extent to which this reflects a difference in the inherent virulence of Omicron, or just higher levels of population immunity, is currently not clear. | |
| medRXiv | Oct 2021 | DP-ACCORD | A novel proxy for the Delta variant, RNA-dependent RNA polymerase target delay in the Seegene Allplex™ 2019-nCoV PCR assay, was associated with higher mortality (adjusted Odds Ratio 1.45 [95%CI 1.13-1.86]), compared to presumptive Beta infection, in the Western Cape, South Africa (April-July 2021). Prior diagnosed infection and vaccination were protective. |
To understand COVID-19 evolution and impact, also on pregnancy and chronic diseases, by applying a data science approach to health data to study the clinical epidemiology and evolution of a new SARS-CoV-2 variant, which emerged in South Africa.