@article{Davies2022,
abstract = {Objectives: 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. Methods: In this cohort study, we included public sector patients aged ≥20 years with a laboratory confirmed COVID-19 diagnosis between 14 November-11 December 2021 (wave four) and equivalent prior wave periods. We compared the risk between waves of the following outcomes using Cox regression: death, severe hospitalization or death and any hospitalization or death (all ≤14 days after diagnosis) adjusted for age, sex, comorbidities, geography, vaccination and prior infection. Results: We included 5,144 patients from wave four and 11,609 from prior waves. Risk of all outcomes was lower in wave four compared to the Delta-driven wave three (adjusted Hazard Ratio (aHR) [95{\%} confidence interval (CI)] for death 0.27 [0.19; 0.38]. Risk reduction was lower when adjusting for vaccination and prior diagnosed infection (aHR:0.41, 95{\%} CI: 0.29; 0.59) and reduced further when accounting for unascertained prior infections (aHR: 0.72). Vaccine protection was maintained in wave four (aHR for outcome of death: 0.24; 95{\%} CI: 0.10; 0.58). Conclusions: In the Omicron-driven wave, severe COVID-19 outcomes were reduced mostly due to protection conferred by prior infection and/or vaccination, but intrinsically reduced virulence may account for an approximately 25{\%} reduced risk of severe hospitalization or death compared to Delta. {\#}{\#}{\#} Competing Interest Statement The authors have declared no competing interest. {\#}{\#}{\#} Funding Statement We acknowledge funding for the Western Cape Provincial Health Data Centre from the Western Cape Department of Health, the US National Institutes for Health (R01 HD080465, U01 AI069924), the Bill and Melinda Gates Foundation (1164272, 119327), the United States Agency for International Development (72067418CA00023), the European Union (101045989), the Wellcome Trust (203135/Z/16/Z, 222574) and the Medical Research Council of South Africa. RJW receives support from the Francis Crick Institute which is funded by Wellcome (FC0010218), MRC (UK) (FC0010218) and Cancer Research UK (FC0010218). He also receives support from Wellcome (203135, 222574) and the Medical Research Council of South Africa. {\#}{\#}{\#} Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Human Research Ethics Committee, University of Cape Town Faculty of Health Sciences, South Africa I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors.},
author = {Davies, Mary-Ann and Kassanjee, Reshma and Rousseau, Petro and Morden, Erna and Johnson, Leigh and Solomon, Wesley and Hsiao, Nei-Yuan and Hussey, Hannah and Meintjes, Graeme A and Paleker, Masudah and Jacobs, Theuns and Raubenheimer, Peter and Heekes, Alexa and Dane, Pierre and Bam, Jamy-Lee and Smith, Mariette and Preiser, Wolfgang and Pienaar, David and Mendelson, Marc and Naude, Jonathan and Schreuder, Neshaad and Mnguni, Ayanda and Roux, Susan Le and Murie, Katie and Prozesky, Hans and Mahomed, Hassan and Rossouw, Liezel and Wasserman, Sean and Maughan, Deborah and Boloko, Linda and Smith, Barry and Taljaard, Jantjie and Symons, Greg and Ntusi, Ntobeko A B and Parker, Arifa and Wolter, Nicole and Jassat, Waasila and Cohen, Cheryl and Lessells, Richard and Wilkinson, Robert J and Arendse, Juanita and Kariem, Saadiq and Moodley, Melvin and Vallabhjee, Krish and Wolmarans, Milani and Boulle, Andrew},
doi = {10.1101/2022.01.12.22269148},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Davies et al. - 2022 - Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous wa.pdf:pdf},
journal = {medRxiv},
keywords = {OA,fund{\_}ack,genomics{\_}fund{\_}ack,original},
mendeley-tags = {OA,fund{\_}ack,genomics{\_}fund{\_}ack,original},
month = {jan},
pages = {2022.01.12.22269148},
pmid = {35043121},
publisher = {Cold Spring Harbor Laboratory Press},
title = {{Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa}},
url = {https://www.medrxiv.org/content/10.1101/2022.01.12.22269148v1 https://www.medrxiv.org/content/10.1101/2022.01.12.22269148v1.abstract},
volume = {13},
year = {2022}
}

{"_id":"HJmXnTYPWwM3FfiwR","bibbaseid":"davies-kassanjee-rousseau-morden-johnson-solomon-hsiao-hussey-etal-outcomesoflaboratoryconfirmedsarscov2infectionintheomicrondrivenfourthwavecomparedwithpreviouswavesinthewesterncapeprovincesouthafrica-2022","author_short":["Davies, M.","Kassanjee, R.","Rousseau, P.","Morden, E.","Johnson, L.","Solomon, W.","Hsiao, N.","Hussey, H.","Meintjes, G. A","Paleker, M.","Jacobs, T.","Raubenheimer, P.","Heekes, A.","Dane, P.","Bam, J.","Smith, M.","Preiser, W.","Pienaar, D.","Mendelson, M.","Naude, J.","Schreuder, N.","Mnguni, A.","Roux, S. L.","Murie, K.","Prozesky, H.","Mahomed, H.","Rossouw, L.","Wasserman, S.","Maughan, D.","Boloko, L.","Smith, B.","Taljaard, J.","Symons, G.","Ntusi, N. A B","Parker, A.","Wolter, N.","Jassat, W.","Cohen, C.","Lessells, R.","Wilkinson, R. J","Arendse, J.","Kariem, S.","Moodley, M.","Vallabhjee, K.","Wolmarans, M.","Boulle, A."],"bibdata":{"bibtype":"article","type":"article","abstract":"Objectives: 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. Methods: In this cohort study, we included public sector patients aged ≥20 years with a laboratory confirmed COVID-19 diagnosis between 14 November-11 December 2021 (wave four) and equivalent prior wave periods. We compared the risk between waves of the following outcomes using Cox regression: death, severe hospitalization or death and any hospitalization or death (all ≤14 days after diagnosis) adjusted for age, sex, comorbidities, geography, vaccination and prior infection. Results: We included 5,144 patients from wave four and 11,609 from prior waves. Risk of all outcomes was lower in wave four compared to the Delta-driven wave three (adjusted Hazard Ratio (aHR) [95% confidence interval (CI)] for death 0.27 [0.19; 0.38]. Risk reduction was lower when adjusting for vaccination and prior diagnosed infection (aHR:0.41, 95% CI: 0.29; 0.59) and reduced further when accounting for unascertained prior infections (aHR: 0.72). Vaccine protection was maintained in wave four (aHR for outcome of death: 0.24; 95% CI: 0.10; 0.58). Conclusions: In the Omicron-driven wave, severe COVID-19 outcomes were reduced mostly due to protection conferred by prior infection and/or vaccination, but intrinsically reduced virulence may account for an approximately 25% reduced risk of severe hospitalization or death compared to Delta. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement We acknowledge funding for the Western Cape Provincial Health Data Centre from the Western Cape Department of Health, the US National Institutes for Health (R01 HD080465, U01 AI069924), the Bill and Melinda Gates Foundation (1164272, 119327), the United States Agency for International Development (72067418CA00023), the European Union (101045989), the Wellcome Trust (203135/Z/16/Z, 222574) and the Medical Research Council of South Africa. RJW receives support from the Francis Crick Institute which is funded by Wellcome (FC0010218), MRC (UK) (FC0010218) and Cancer Research UK (FC0010218). He also receives support from Wellcome (203135, 222574) and the Medical Research Council of South Africa. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Human Research Ethics Committee, University of Cape Town Faculty of Health Sciences, South Africa I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors.","author":[{"propositions":[],"lastnames":["Davies"],"firstnames":["Mary-Ann"],"suffixes":[]},{"propositions":[],"lastnames":["Kassanjee"],"firstnames":["Reshma"],"suffixes":[]},{"propositions":[],"lastnames":["Rousseau"],"firstnames":["Petro"],"suffixes":[]},{"propositions":[],"lastnames":["Morden"],"firstnames":["Erna"],"suffixes":[]},{"propositions":[],"lastnames":["Johnson"],"firstnames":["Leigh"],"suffixes":[]},{"propositions":[],"lastnames":["Solomon"],"firstnames":["Wesley"],"suffixes":[]},{"propositions":[],"lastnames":["Hsiao"],"firstnames":["Nei-Yuan"],"suffixes":[]},{"propositions":[],"lastnames":["Hussey"],"firstnames":["Hannah"],"suffixes":[]},{"propositions":[],"lastnames":["Meintjes"],"firstnames":["Graeme","A"],"suffixes":[]},{"propositions":[],"lastnames":["Paleker"],"firstnames":["Masudah"],"suffixes":[]},{"propositions":[],"lastnames":["Jacobs"],"firstnames":["Theuns"],"suffixes":[]},{"propositions":[],"lastnames":["Raubenheimer"],"firstnames":["Peter"],"suffixes":[]},{"propositions":[],"lastnames":["Heekes"],"firstnames":["Alexa"],"suffixes":[]},{"propositions":[],"lastnames":["Dane"],"firstnames":["Pierre"],"suffixes":[]},{"propositions":[],"lastnames":["Bam"],"firstnames":["Jamy-Lee"],"suffixes":[]},{"propositions":[],"lastnames":["Smith"],"firstnames":["Mariette"],"suffixes":[]},{"propositions":[],"lastnames":["Preiser"],"firstnames":["Wolfgang"],"suffixes":[]},{"propositions":[],"lastnames":["Pienaar"],"firstnames":["David"],"suffixes":[]},{"propositions":[],"lastnames":["Mendelson"],"firstnames":["Marc"],"suffixes":[]},{"propositions":[],"lastnames":["Naude"],"firstnames":["Jonathan"],"suffixes":[]},{"propositions":[],"lastnames":["Schreuder"],"firstnames":["Neshaad"],"suffixes":[]},{"propositions":[],"lastnames":["Mnguni"],"firstnames":["Ayanda"],"suffixes":[]},{"propositions":[],"lastnames":["Roux"],"firstnames":["Susan","Le"],"suffixes":[]},{"propositions":[],"lastnames":["Murie"],"firstnames":["Katie"],"suffixes":[]},{"propositions":[],"lastnames":["Prozesky"],"firstnames":["Hans"],"suffixes":[]},{"propositions":[],"lastnames":["Mahomed"],"firstnames":["Hassan"],"suffixes":[]},{"propositions":[],"lastnames":["Rossouw"],"firstnames":["Liezel"],"suffixes":[]},{"propositions":[],"lastnames":["Wasserman"],"firstnames":["Sean"],"suffixes":[]},{"propositions":[],"lastnames":["Maughan"],"firstnames":["Deborah"],"suffixes":[]},{"propositions":[],"lastnames":["Boloko"],"firstnames":["Linda"],"suffixes":[]},{"propositions":[],"lastnames":["Smith"],"firstnames":["Barry"],"suffixes":[]},{"propositions":[],"lastnames":["Taljaard"],"firstnames":["Jantjie"],"suffixes":[]},{"propositions":[],"lastnames":["Symons"],"firstnames":["Greg"],"suffixes":[]},{"propositions":[],"lastnames":["Ntusi"],"firstnames":["Ntobeko","A","B"],"suffixes":[]},{"propositions":[],"lastnames":["Parker"],"firstnames":["Arifa"],"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":["Arendse"],"firstnames":["Juanita"],"suffixes":[]},{"propositions":[],"lastnames":["Kariem"],"firstnames":["Saadiq"],"suffixes":[]},{"propositions":[],"lastnames":["Moodley"],"firstnames":["Melvin"],"suffixes":[]},{"propositions":[],"lastnames":["Vallabhjee"],"firstnames":["Krish"],"suffixes":[]},{"propositions":[],"lastnames":["Wolmarans"],"firstnames":["Milani"],"suffixes":[]},{"propositions":[],"lastnames":["Boulle"],"firstnames":["Andrew"],"suffixes":[]}],"doi":"10.1101/2022.01.12.22269148","file":":C$\\$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Davies et al. - 2022 - Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous wa.pdf:pdf","journal":"medRxiv","keywords":"OA,fund_ack,genomics_fund_ack,original","mendeley-tags":"OA,fund_ack,genomics_fund_ack,original","month":"jan","pages":"2022.01.12.22269148","pmid":"35043121","publisher":"Cold Spring Harbor Laboratory Press","title":"Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa","url":"https://www.medrxiv.org/content/10.1101/2022.01.12.22269148v1 https://www.medrxiv.org/content/10.1101/2022.01.12.22269148v1.abstract","volume":"13","year":"2022","bibtex":"@article{Davies2022,\r\nabstract = {Objectives: 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. Methods: In this cohort study, we included public sector patients aged ≥20 years with a laboratory confirmed COVID-19 diagnosis between 14 November-11 December 2021 (wave four) and equivalent prior wave periods. We compared the risk between waves of the following outcomes using Cox regression: death, severe hospitalization or death and any hospitalization or death (all ≤14 days after diagnosis) adjusted for age, sex, comorbidities, geography, vaccination and prior infection. Results: We included 5,144 patients from wave four and 11,609 from prior waves. Risk of all outcomes was lower in wave four compared to the Delta-driven wave three (adjusted Hazard Ratio (aHR) [95{\\%} confidence interval (CI)] for death 0.27 [0.19; 0.38]. Risk reduction was lower when adjusting for vaccination and prior diagnosed infection (aHR:0.41, 95{\\%} CI: 0.29; 0.59) and reduced further when accounting for unascertained prior infections (aHR: 0.72). Vaccine protection was maintained in wave four (aHR for outcome of death: 0.24; 95{\\%} CI: 0.10; 0.58). Conclusions: In the Omicron-driven wave, severe COVID-19 outcomes were reduced mostly due to protection conferred by prior infection and/or vaccination, but intrinsically reduced virulence may account for an approximately 25{\\%} reduced risk of severe hospitalization or death compared to Delta. {\\#}{\\#}{\\#} Competing Interest Statement The authors have declared no competing interest. {\\#}{\\#}{\\#} Funding Statement We acknowledge funding for the Western Cape Provincial Health Data Centre from the Western Cape Department of Health, the US National Institutes for Health (R01 HD080465, U01 AI069924), the Bill and Melinda Gates Foundation (1164272, 119327), the United States Agency for International Development (72067418CA00023), the European Union (101045989), the Wellcome Trust (203135/Z/16/Z, 222574) and the Medical Research Council of South Africa. RJW receives support from the Francis Crick Institute which is funded by Wellcome (FC0010218), MRC (UK) (FC0010218) and Cancer Research UK (FC0010218). He also receives support from Wellcome (203135, 222574) and the Medical Research Council of South Africa. {\\#}{\\#}{\\#} Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Human Research Ethics Committee, University of Cape Town Faculty of Health Sciences, South Africa I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors.},\r\nauthor = {Davies, Mary-Ann and Kassanjee, Reshma and Rousseau, Petro and Morden, Erna and Johnson, Leigh and Solomon, Wesley and Hsiao, Nei-Yuan and Hussey, Hannah and Meintjes, Graeme A and Paleker, Masudah and Jacobs, Theuns and Raubenheimer, Peter and Heekes, Alexa and Dane, Pierre and Bam, Jamy-Lee and Smith, Mariette and Preiser, Wolfgang and Pienaar, David and Mendelson, Marc and Naude, Jonathan and Schreuder, Neshaad and Mnguni, Ayanda and Roux, Susan Le and Murie, Katie and Prozesky, Hans and Mahomed, Hassan and Rossouw, Liezel and Wasserman, Sean and Maughan, Deborah and Boloko, Linda and Smith, Barry and Taljaard, Jantjie and Symons, Greg and Ntusi, Ntobeko A B and Parker, Arifa and Wolter, Nicole and Jassat, Waasila and Cohen, Cheryl and Lessells, Richard and Wilkinson, Robert J and Arendse, Juanita and Kariem, Saadiq and Moodley, Melvin and Vallabhjee, Krish and Wolmarans, Milani and Boulle, Andrew},\r\ndoi = {10.1101/2022.01.12.22269148},\r\nfile = {:C$\\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Davies et al. - 2022 - Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous wa.pdf:pdf},\r\njournal = {medRxiv},\r\nkeywords = {OA,fund{\\_}ack,genomics{\\_}fund{\\_}ack,original},\r\nmendeley-tags = {OA,fund{\\_}ack,genomics{\\_}fund{\\_}ack,original},\r\nmonth = {jan},\r\npages = {2022.01.12.22269148},\r\npmid = {35043121},\r\npublisher = {Cold Spring Harbor Laboratory Press},\r\ntitle = {{Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa}},\r\nurl = {https://www.medrxiv.org/content/10.1101/2022.01.12.22269148v1 https://www.medrxiv.org/content/10.1101/2022.01.12.22269148v1.abstract},\r\nvolume = {13},\r\nyear = {2022}\r\n}\r\n","author_short":["Davies, M.","Kassanjee, R.","Rousseau, P.","Morden, E.","Johnson, L.","Solomon, W.","Hsiao, N.","Hussey, H.","Meintjes, G. 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