@article{Hussey2022a,
abstract = {Abstract Background The extent to which the reduced risk of severe disease seen with SARS-CoV-2 Omicron is due to a decrease in variant virulence, or higher levels of population immunity, is currently not clear. Methods RdRp target delay (RTD) in the Seegene AllplexTM 2019-nCoV PCR assay is a proxy marker for the Delta variant. The absence of this proxy marker in the transition period was used to identify suspected Omicron infections. Cox regression was performed for the outcome of hospital admission in those who tested positive for SARS-CoV-2 on the Seegene AllplexTM assay from 1 November to 14 December 2021 in the Western Cape Province, South Africa, public sector. Vaccination status and prior diagnosed infection, were adjusted for. Results 150 cases with RTD and 1486 cases without RTD were included. Cases without RTD had a lower hazard of admission (adjusted Hazard Ratio [aHR] of 0.56, 95{\%}CI 0.34-0.91). Complete vaccination was protective of admission with an aHR of 0.45 (95{\%}CI 0.26-0.77). Conclusion Omicron has resulted in a lower risk of hospital admission, compared to contemporaneous Delta infection, when using the proxy marker of RTD. Under-ascertainment of reinfections with an immune escape variant remains a challenge to accurately assessing variant virulence.},
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, Wolfgang and Maponga, Tongai and Iranzadeh, Arash and Wasserman, Sean and Boloko, Linda and Symons, Greg and Raubenheimer, Peter and Parker, Arifa and Schrueder, Neshaad and Solomon, Wesley and Rousseau, Petro and Wolter, Nicole and Jassat, Waasila and Cohen, Cheryl and Lessells, Richard and Wilkinson, Robert J and Boulle, Andrew and Hsiao, Nei-yuan},
doi = {10.1016/J.IJID.2022.02.051},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Hussey et al. - 2022 - Assessing the clinical severity of the Omicron variant in the Western Cape Province, South Africa, using the d(2).pdf:pdf},
issn = {1201-9712},
journal = {International Journal of Infectious Diseases},
keywords = {OA,Omicron variant,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 = {feb},
pages = {150--154},
pmid = {35235826},
publisher = {Elsevier},
title = {{Assessing the clinical severity of the Omicron variant in the Western Cape Province, South Africa, using the diagnostic PCR proxy marker of RdRp target delay to distinguish between Omicron and Delta infections – a survival analysis}},
url = {http://www.ijidonline.com/article/S1201971222001291/fulltext http://www.ijidonline.com/article/S1201971222001291/abstract https://www.ijidonline.com/article/S1201-9712(22)00129-1/abstract},
volume = {118},
year = {2022}
}

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Methods RdRp target delay (RTD) in the Seegene AllplexTM 2019-nCoV PCR assay is a proxy marker for the Delta variant. The absence of this proxy marker in the transition period was used to identify suspected Omicron infections. Cox regression was performed for the outcome of hospital admission in those who tested positive for SARS-CoV-2 on the Seegene AllplexTM assay from 1 November to 14 December 2021 in the Western Cape Province, South Africa, public sector. Vaccination status and prior diagnosed infection, were adjusted for. Results 150 cases with RTD and 1486 cases without RTD were included. Cases without RTD had a lower hazard of admission (adjusted Hazard Ratio [aHR] of 0.56, 95%CI 0.34-0.91). Complete vaccination was protective of admission with an aHR of 0.45 (95%CI 0.26-0.77). Conclusion Omicron has resulted in a lower risk of hospital admission, compared to contemporaneous Delta infection, when using the proxy marker of RTD. Under-ascertainment of reinfections with an immune escape variant remains a challenge to accurately assessing variant virulence.","author":[{"propositions":[],"lastnames":["Hussey"],"firstnames":["Hannah"],"suffixes":[]},{"propositions":[],"lastnames":["Davies"],"firstnames":["Mary-Ann"],"suffixes":[]},{"propositions":[],"lastnames":["Heekes"],"firstnames":["Alexa"],"suffixes":[]},{"propositions":[],"lastnames":["Williamson"],"firstnames":["Carolyn"],"suffixes":[]},{"propositions":[],"lastnames":["Valley-Omar"],"firstnames":["Ziyaad"],"suffixes":[]},{"propositions":[],"lastnames":["Hardie"],"firstnames":["Diana"],"suffixes":[]},{"propositions":[],"lastnames":["Korsman"],"firstnames":["Stephen"],"suffixes":[]},{"propositions":[],"lastnames":["Doolabh"],"firstnames":["Deelan"],"suffixes":[]},{"propositions":[],"lastnames":["Preiser"],"firstnames":["Wolfgang"],"suffixes":[]},{"propositions":[],"lastnames":["Maponga"],"firstnames":["Tongai"],"suffixes":[]},{"propositions":[],"lastnames":["Iranzadeh"],"firstnames":["Arash"],"suffixes":[]},{"propositions":[],"lastnames":["Wasserman"],"firstnames":["Sean"],"suffixes":[]},{"propositions":[],"lastnames":["Boloko"],"firstnames":["Linda"],"suffixes":[]},{"propositions":[],"lastnames":["Symons"],"firstnames":["Greg"],"suffixes":[]},{"propositions":[],"lastnames":["Raubenheimer"],"firstnames":["Peter"],"suffixes":[]},{"propositions":[],"lastnames":["Parker"],"firstnames":["Arifa"],"suffixes":[]},{"propositions":[],"lastnames":["Schrueder"],"firstnames":["Neshaad"],"suffixes":[]},{"propositions":[],"lastnames":["Solomon"],"firstnames":["Wesley"],"suffixes":[]},{"propositions":[],"lastnames":["Rousseau"],"firstnames":["Petro"],"suffixes":[]},{"propositions":[],"lastnames":["Wolter"],"firstnames":["Nicole"],"suffixes":[]},{"propositions":[],"lastnames":["Jassat"],"firstnames":["Waasila"],"suffixes":[]},{"propositions":[],"lastnames":["Cohen"],"firstnames":["Cheryl"],"suffixes":[]},{"propositions":[],"lastnames":["Lessells"],"firstnames":["Richard"],"suffixes":[]},{"propositions":[],"lastnames":["Wilkinson"],"firstnames":["Robert","J"],"suffixes":[]},{"propositions":[],"lastnames":["Boulle"],"firstnames":["Andrew"],"suffixes":[]},{"propositions":[],"lastnames":["Hsiao"],"firstnames":["Nei-yuan"],"suffixes":[]}],"doi":"10.1016/J.IJID.2022.02.051","file":":C$\\$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Hussey et al. - 2022 - Assessing the clinical severity of the Omicron variant in the Western Cape Province, South Africa, using the d(2).pdf:pdf","issn":"1201-9712","journal":"International Journal of Infectious Diseases","keywords":"OA,Omicron variant,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":"feb","pages":"150–154","pmid":"35235826","publisher":"Elsevier","title":"Assessing the clinical severity of the Omicron variant in the Western Cape Province, South Africa, using the diagnostic PCR proxy marker of RdRp target delay to distinguish between Omicron and Delta infections – a survival analysis","url":"http://www.ijidonline.com/article/S1201971222001291/fulltext http://www.ijidonline.com/article/S1201971222001291/abstract https://www.ijidonline.com/article/S1201-9712(22)00129-1/abstract","volume":"118","year":"2022","bibtex":"@article{Hussey2022a,\r\nabstract = {Abstract Background The extent to which the reduced risk of severe disease seen with SARS-CoV-2 Omicron is due to a decrease in variant virulence, or higher levels of population immunity, is currently not clear. Methods RdRp target delay (RTD) in the Seegene AllplexTM 2019-nCoV PCR assay is a proxy marker for the Delta variant. The absence of this proxy marker in the transition period was used to identify suspected Omicron infections. Cox regression was performed for the outcome of hospital admission in those who tested positive for SARS-CoV-2 on the Seegene AllplexTM assay from 1 November to 14 December 2021 in the Western Cape Province, South Africa, public sector. Vaccination status and prior diagnosed infection, were adjusted for. Results 150 cases with RTD and 1486 cases without RTD were included. Cases without RTD had a lower hazard of admission (adjusted Hazard Ratio [aHR] of 0.56, 95{\\%}CI 0.34-0.91). Complete vaccination was protective of admission with an aHR of 0.45 (95{\\%}CI 0.26-0.77). Conclusion Omicron has resulted in a lower risk of hospital admission, compared to contemporaneous Delta infection, when using the proxy marker of RTD. Under-ascertainment of reinfections with an immune escape variant remains a challenge to accurately assessing variant virulence.},\r\nauthor = {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, Wolfgang and Maponga, Tongai and Iranzadeh, Arash and Wasserman, Sean and Boloko, Linda and Symons, Greg and Raubenheimer, Peter and Parker, Arifa and Schrueder, Neshaad and Solomon, Wesley and Rousseau, Petro and Wolter, Nicole and Jassat, Waasila and Cohen, Cheryl and Lessells, Richard and Wilkinson, Robert J and Boulle, Andrew and Hsiao, Nei-yuan},\r\ndoi = {10.1016/J.IJID.2022.02.051},\r\nfile = {:C$\\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Hussey et al. - 2022 - Assessing the clinical severity of the Omicron variant in the Western Cape Province, South Africa, using the d(2).pdf:pdf},\r\nissn = {1201-9712},\r\njournal = {International Journal of Infectious Diseases},\r\nkeywords = {OA,Omicron variant,RdRp target delay,SARS-CoV-2,South Africa,clinical severity,fund{\\_}ack,genomics{\\_}fund{\\_}ack,original},\r\nmendeley-tags = {OA,fund{\\_}ack,genomics{\\_}fund{\\_}ack,original},\r\nmonth = {feb},\r\npages = {150--154},\r\npmid = {35235826},\r\npublisher = {Elsevier},\r\ntitle = {{Assessing the clinical severity of the Omicron variant in the Western Cape Province, South Africa, using the diagnostic PCR proxy marker of RdRp target delay to distinguish between Omicron and Delta infections – a survival analysis}},\r\nurl = {http://www.ijidonline.com/article/S1201971222001291/fulltext http://www.ijidonline.com/article/S1201971222001291/abstract https://www.ijidonline.com/article/S1201-9712(22)00129-1/abstract},\r\nvolume = {118},\r\nyear = {2022}\r\n}\r\n","author_short":["Hussey, H.","Davies, M.","Heekes, A.","Williamson, C.","Valley-Omar, Z.","Hardie, D.","Korsman, S.","Doolabh, D.","Preiser, W.","Maponga, T.","Iranzadeh, A.","Wasserman, S.","Boloko, L.","Symons, G.","Raubenheimer, P.","Parker, A.","Schrueder, N.","Solomon, W.","Rousseau, P.","Wolter, N.","Jassat, W.","Cohen, C.","Lessells, R.","Wilkinson, R. 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