Higher mortality associated with the SARS-CoV-2 Delta variant in the Western Cape, South Africa, using RdRp target delay as a proxy: a cross-sectional study. [version 1; peer review: 2 approved]. Hussey, H., Davies, M., Heekes, A., Williamson, C., Valley-Omar, Z., Hardie, D., Korsman, S., Doolabh, D., Preiser, W., Maponga, T., Iranzadeh, A., Engelbrecht, S., Wasserman, S., Schrueder, N., Boloko, L., Symons, G., Raubenheimer, P., Viljoen, A., Parker, A., Cohen, C., Jasat, W., Lessells, R., Wilkinson, R. J, Boulle, A., & Hsiao, M. Gates Open Research, 6:117, F1000 Research Limited, aug, 2022.
Higher mortality associated with the SARS-CoV-2 Delta variant in the Western Cape, South Africa, using RdRp target delay as a proxy: a cross-sectional study. [version 1; peer review: 2 approved] [link]Paper  doi  abstract   bibtex   
Background: The SARS-CoV-2 Delta variant (B.1.617.2) has been associated with more severe disease, particularly when compared to the Alpha variant. Most of this data, however, is from high income countries and less is understood about the variant's disease severity in other settings, particularly in an African context, and when compared to the Beta variant. Methods: A novel proxy marker, RNA-dependent RNA polymerase (RdRp) target delay in the Seegene Allplex TM 2019-nCoV (polymerase chain reaction) PCR assay, was used to identify suspected Delta variant infection in routine laboratory data. All cases diagnosed on this assay in the public sector in the Western Cape, South Africa, from 1 April to 31 July 2021, were included in the dataset provided by the Western Cape Provincial Health Data Centre (PHDC). The PHDC collates information on all COVID-19 related laboratory tests, hospital admissions and deaths for the province. Odds ratios for the association between the proxy marker and death were calculated, adjusted for prior diagnosed infection and vaccination status. Results: A total of 11,355 cases with 700 deaths were included in this study. RdRp target delay (suspected Delta variant) was associated with higher mortality (adjusted odds ratio [aOR] 1.45; 95% confidence interval [CI]: 1.13-1.86), compared to presumptive Beta infection. Prior diagnosed infection during the previous COVID-19 wave, which was driven by the Beta variant, was protective (aOR 0.32; 95%CI: 0.11-0.92) as was vaccination (aOR [95%CI] 0.15 [0.03-0.62] for complete vaccination [≥28 days post a single dose of Ad26.COV2.S or ≥14 days post second BNT162b2 dose]). Conclusion: RdRp target delay, a proxy for infection with the Delta variant, is associated with an increased risk of mortality amongst those who were tested for COVID-19 in our setting.
@article{Hussey2022b,
abstract = {Background: The SARS-CoV-2 Delta variant (B.1.617.2) has been associated with more severe disease, particularly when compared to the Alpha variant. Most of this data, however, is from high income countries and less is understood about the variant's disease severity in other settings, particularly in an African context, and when compared to the Beta variant. Methods: A novel proxy marker, RNA-dependent RNA polymerase (RdRp) target delay in the Seegene Allplex TM 2019-nCoV (polymerase chain reaction) PCR assay, was used to identify suspected Delta variant infection in routine laboratory data. All cases diagnosed on this assay in the public sector in the Western Cape, South Africa, from 1 April to 31 July 2021, were included in the dataset provided by the Western Cape Provincial Health Data Centre (PHDC). The PHDC collates information on all COVID-19 related laboratory tests, hospital admissions and deaths for the province. Odds ratios for the association between the proxy marker and death were calculated, adjusted for prior diagnosed infection and vaccination status. Results: A total of 11,355 cases with 700 deaths were included in this study. RdRp target delay (suspected Delta variant) was associated with higher mortality (adjusted odds ratio [aOR] 1.45; 95{\%} confidence interval [CI]: 1.13-1.86), compared to presumptive Beta infection. Prior diagnosed infection during the previous COVID-19 wave, which was driven by the Beta variant, was protective (aOR 0.32; 95{\%}CI: 0.11-0.92) as was vaccination (aOR [95{\%}CI] 0.15 [0.03-0.62] for complete vaccination [≥28 days post a single dose of Ad26.COV2.S or ≥14 days post second BNT162b2 dose]). Conclusion: RdRp target delay, a proxy for infection with the Delta variant, is associated with an increased risk of mortality amongst those who were tested for COVID-19 in our setting.},
author = {Hussey, Hannah and Davies, Mary-Ann and Heekes, Alexa and Williamson, Carolyn and Valley-Omar, Ziyaad and Hardie, Diana and Korsman, Stephen and Doolabh, Deelan and Preiser, Wofgang and Maponga, Tongai and Iranzadeh, Arash and Engelbrecht, Susan and Wasserman, Sean and Schrueder, Neshaad and Boloko, Linda and Symons, Greg and Raubenheimer, Peter and Viljoen, Abraham and Parker, Arifa and Cohen, Cheryl and Jasat, Waasila and Lessells, Richard and Wilkinson, Robert J and Boulle, Andrew and Hsiao, Marvin},
doi = {10.12688/gatesopenres.13654.1},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Hussey et al. - 2022 - Higher mortality associated with the SARS-CoV-2 Delta variant in the Western Cape, South Africa, using RdRp targe.pdf:pdf},
journal = {Gates Open Research},
keywords = {B.1.617.2,Delta,OA,RdRp target delay,SARS-CoV-2,South Africa,clinical severity,fund{\_}ack,genomics{\_}fund{\_}ack,original},
mendeley-tags = {OA,fund{\_}ack,genomics{\_}fund{\_}ack,original},
month = {aug},
pages = {117},
pmid = {37994361},
publisher = {F1000 Research Limited},
title = {{Higher mortality associated with the SARS-CoV-2 Delta variant in the Western Cape, South Africa, using RdRp target delay as a proxy: a cross-sectional study. [version 1; peer review: 2 approved]}},
url = {https://gatesopenresearch.org/articles/6-117},
volume = {6},
year = {2022}
}
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