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Audley G, Raubenheimer P, Symons G, Mendelson M, Meintjes G, Ntusi NAB, Wasserman S, Dlamini S, Dheda K, van Zyl-Smit R, Calligaro G. High-flow nasal oxygen in resource-constrained, non-intensive, high-care wards for COVID-19 acute hypoxaemic respiratory failure: Comparing outcomes of the first v. third waves at a tertiary centre in South Africa. Afr J Thorac Crit Care Med 2024; 30:e1151. [PMID: 38756391 PMCID: PMC11094705 DOI: 10.7196/ajtccm.2024.v30i1.1151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 01/08/2024] [Indexed: 05/18/2024] Open
Abstract
Background High-flow nasal oxygen (HFNO) is an accepted treatment for severe COVID-19-related acute hypoxaemic respiratory failure (AHRF). Objectives To determine whether treatment outcomes at Groote Schuur Hospital, Cape Town, South Africa, during the third COVID-19 wave would be affected by increased institutional experience and capacity for HNFO and more restrictive admission criteria for respiratory high-care wards and intensive care units. Methods We included consecutive patients with COVID-19-related AHRF treated with HFNO during the first and third COVID-19 waves. The primary endpoint was comparison of HFNO failure (composite of the need for intubation or death while on HFNO) between waves. Results A total of 744 patients were included: 343 in the first COVID-19 wave and 401 in the third. Patients treated with HFNO in the first wave were older (median (interquartile range) age 53 (46 - 61) years v. 47 (40 - 56) years; p<0.001), and had higher prevalences of diabetes (46.9% v. 36.9%; p=0.006), hypertension (51.0% v. 35.2%; p<0.001), obesity (33.5% v. 26.2%; p=0.029) and HIV infection (12.5% v. 5.5%; p<0.001). The partial pressure of arterial oxygen to fraction of inspired oxygen (PaO2 /FiO2 ) ratio at HFNO initiation and the ratio of oxygen saturation/FiO2 to respiratory rate within 6 hours (ROX-6 score) after HFNO commencement were lower in the first wave compared with the third (median 57.9 (47.3 - 74.3) mmHg v. 64.3 (51.2 - 79.0) mmHg; p=0.005 and 3.19 (2.37 - 3.77) v. 3.43 (2.93 - 4.00); p<0.001, respectively). The likelihood of HFNO failure (57.1% v. 59.6%; p=0.498) and mortality (46.9% v. 52.1%; p=0.159) did not differ significantly between the first and third waves. Conclusion Despite differences in patient characteristics, circulating viral variant and institutional experience with HFNO, treatment outcomes were very similar in the first and third COVID-19 waves. We conclude that once AHRF is established in COVID-19 pneumonia, the comorbidity profile and HFNO provider experience do not appear to affect outcome. Study synopsis What the study adds. This study adds to the body of evidence demonstrating the utility of high-flow nasal oxygen (HFNO) in avoiding invasive mechanical ventilation (IMV) in patients with severe COVID-19 hypoxaemic respiratory failure, and shows that this utility remained consistent across different waves of the COVID-19 pandemic.Implications of the study. In resource-constrained settings, HFNO is a feasible non-invasive alternative to IMV and can be employed with favourable and consistent outcomes outside traditional critical care wards. It also confirms that the degree of gas exchange abnormality, and not pre-existing patient-related factors, circulating wave variant or provider experience, is the main predictor of HFNO failure.
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Affiliation(s)
- G Audley
- Division of General Internal Medicine, Department of Medicine, Faculty of Health Sciences, University of Cape Town and Groote Schuur
Hospital, Cape Town, South Africa
| | - P Raubenheimer
- Division of General Internal Medicine, Department of Medicine, Faculty of Health Sciences, University of Cape Town and Groote Schuur
Hospital, Cape Town, South Africa
| | - G Symons
- Division of General Internal Medicine, Department of Medicine, Faculty of Health Sciences, University of Cape Town and Groote Schuur
Hospital, Cape Town, South Africa
- Division of Pulmonology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - M Mendelson
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Faculty of Health Sciences, University of Cape Town and Groote
Schuur Hospital, Cape Town, South Africa
| | - G Meintjes
- Division of General Internal Medicine, Department of Medicine, Faculty of Health Sciences, University of Cape Town and Groote Schuur
Hospital, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town,
South Africa
| | - N A B Ntusi
- Division of General Internal Medicine, Department of Medicine, Faculty of Health Sciences, University of Cape Town and Groote Schuur
Hospital, Cape Town, South Africa
- Division of Cardiology, Department of Medicine, Faculty of Health Sciences, University of Cape Town and Groote Schuur Hospital, Cape Town,
South Africa
- South African Medical Research Council/University of Cape Town Extramural Research Unit on the Intersection of Noncommunicable Diseases
and Infectious Diseases, University of Cape Town, South Africa
| | - S Wasserman
- Division of General Internal Medicine, Department of Medicine, Faculty of Health Sciences, University of Cape Town and Groote Schuur
Hospital, Cape Town, South Africa
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Faculty of Health Sciences, University of Cape Town and Groote
Schuur Hospital, Cape Town, South Africa
| | - S Dlamini
- Division of General Internal Medicine, Department of Medicine, Faculty of Health Sciences, University of Cape Town and Groote Schuur
Hospital, Cape Town, South Africa
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Faculty of Health Sciences, University of Cape Town and Groote
Schuur Hospital, Cape Town, South Africa
| | - K Dheda
- Division of Pulmonology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
- South African Medical Research Council/University of Cape Town Extramural Research Unit on the Intersection of Noncommunicable Diseases
and Infectious Diseases, University of Cape Town, South Africa
- Faculty of Infectious and Tropical Diseases, Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute, University of Cape Town,
South Africa; South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, South Africa
| | - R van Zyl-Smit
- Division of Pulmonology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - G Calligaro
- Division of Pulmonology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute, University of Cape Town,
South Africa; South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, South Africa
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2
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Davies MA, Morden E, Rousseau P, Arendse J, Bam JL, Boloko L, Cloete K, Cohen C, Chetty N, Dane P, Heekes A, Hsiao NY, Hunter M, Hussey H, Jacobs T, Jassat W, Kariem S, Kassanjee R, Laenen I, Roux SL, Lessells R, Mahomed H, Maughan D, Meintjes G, Mendelson M, Mnguni A, Moodley M, Murie K, Naude J, Ntusi NA, Paleker M, Parker A, Pienaar D, Preiser W, Prozesky H, Raubenheimer P, Rossouw L, Schrueder N, Smith B, Smith M, Solomon W, Symons G, Taljaard J, Wasserman S, Wilkinson RJ, Wolmarans M, Wolter N, Boulle A. Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa. Int J Infect Dis 2023; 127:63-68. [PMID: 36436752 PMCID: PMC9686046 DOI: 10.1016/j.ijid.2022.11.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/28/2022] [Accepted: 11/19/2022] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVES We aimed to compare the 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. METHODS We included public sector patients aged ≥20 years with laboratory-confirmed COVID-19 between May 01-May 21, 2022 (BA.4/BA.5 wave) and equivalent previous wave periods. We compared the risk between waves of (i) death and (ii) severe hospitalization/death (all within 21 days of diagnosis) using Cox regression adjusted for demographics, comorbidities, admission pressure, vaccination, and previous infection. RESULTS Among 3793 patients from the BA.4/BA.5 wave and 190,836 patients from previous waves, the risk of severe hospitalization/death was similar in the BA.4/BA.5 and BA.1 waves (adjusted hazard ratio [aHR] 1.12; 95% confidence interval [CI] 0.93; 1.34). Both Omicron waves had a lower risk of severe outcomes than previous waves. Previous infection (aHR 0.29, 95% CI 0.24; 0.36) and vaccination (aHR 0.17; 95% CI 0.07; 0.40 for at least three doses vs no vaccine) were protective. CONCLUSION Disease severity was similar among diagnosed COVID-19 cases in the BA.4/BA.5 and BA.1 periods in the context of growing immunity against SARS-CoV-2 due to previous infection and vaccination, both of which were strongly protective.
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Affiliation(s)
- Mary-Ann Davies
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa,Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa,Corresponding author: Mary-Ann Davies University of Cape Town, Faculty of Health Sciences, Anzio Road, Observatory, 7925, Cape Town, South Africa
| | - Erna Morden
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Jamy-Lee Bam
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa
| | - Linda Boloko
- Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa,Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Keith Cloete
- Western Cape Government: Health, Cape Town, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Chetty
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Pierre Dane
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Alexa Heekes
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Nei-Yuan Hsiao
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa,National Health Laboratory Service, South Africa
| | - Mehreen Hunter
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Hannah Hussey
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa,Metro Health Services, Western Cape Government: Health, Cape Town, South Africa
| | - Theuns Jacobs
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa
| | - Waasila Jassat
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Saadiq Kariem
- Western Cape Government: Health, Cape Town, South Africa
| | - Reshma Kassanjee
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Inneke Laenen
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Division of Health Systems and Public Health, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Sue Le Roux
- Western Cape Government: Health, Cape Town, South Africa,Karl Bremer Hospital, Western Cape Government: Health, Cape Town, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
| | - Hassan Mahomed
- Metro Health Services, Western Cape Government: Health, Cape Town, South Africa,Division of Health Systems and Public Health, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Deborah Maughan
- Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa,Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Graeme Meintjes
- Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa,Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Marc Mendelson
- Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa,Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Ayanda Mnguni
- Khayelitsha District Hospital, Western Cape Government: Health, Cape Town, South Africa
| | - Melvin Moodley
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa
| | - Katy Murie
- Western Cape Government: Health, Cape Town, South Africa,Metro Health Services, Western Cape Government: Health, Cape Town, South Africa
| | - Jonathan Naude
- Mitchells Plain Hospital, Western Cape Government: Health, Cape Town, South Africa
| | - Ntobeko A.B. Ntusi
- Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa,Department of Medicine, University of Cape Town, Cape Town, South Africa,South African Medical Research Council Extramural Unit on Intersection of Noncommunicable Diseases and Infectious Diseases, Cape Town, South Africa
| | - Masudah Paleker
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Division of Health Systems and Public Health, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Arifa Parker
- Tygerberg Hospital, Western Cape Government: Health, Cape Town, South Africa,Division of Infectious Diseases, Department of Medicine, Stellenbosch University, Stellenbosch, South Africa,Division of General Medicine, Department of Medicine, Stellenbosch University, Stellenbosch, South Africa
| | - David Pienaar
- Rural Health Services, Western Cape Government: Health, Cape Town, South Africa
| | - Wolfgang Preiser
- National Health Laboratory Service, South Africa,Division of Medical Virology, University of Stellenbosch, Stellenbosch, South Africa
| | - Hans Prozesky
- Tygerberg Hospital, Western Cape Government: Health, Cape Town, South Africa,Division of Infectious Diseases, Department of Medicine, Stellenbosch University, Stellenbosch, South Africa
| | - Peter Raubenheimer
- Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa,Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Liezel Rossouw
- Western Cape Government: Health, Cape Town, South Africa
| | - Neshaad Schrueder
- Tygerberg Hospital, Western Cape Government: Health, Cape Town, South Africa,Division of General Medicine, Department of Medicine, Stellenbosch University, Stellenbosch, South Africa
| | - Barry Smith
- Western Cape Government: Health, Cape Town, South Africa,Karl Bremer Hospital, Western Cape Government: Health, Cape Town, South Africa
| | - Mariette Smith
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Greg Symons
- Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa,Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Jantjie Taljaard
- Tygerberg Hospital, Western Cape Government: Health, Cape Town, South Africa,Division of Infectious Diseases, Department of Medicine, Stellenbosch University, Stellenbosch, South Africa
| | - Sean Wasserman
- Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa,Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa,Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Robert J. Wilkinson
- The Francis Crick Institute, London, UK,Department of Infectious Diseases, Imperial College London, London, UK,Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Nicole Wolter
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa,School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Andrew Boulle
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa,Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa,Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
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Hussey H, Davies MA, 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 RJ, Boulle A, Hsiao M. 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. Gates Open Res 2022; 6:117. [PMID: 37994361 PMCID: PMC10663174 DOI: 10.12688/gatesopenres.13654.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2022] [Indexed: 11/24/2023] Open
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.
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Affiliation(s)
- Hannah Hussey
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Mary-Ann Davies
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Alexa Heekes
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Carolyn Williamson
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | - Ziyaad Valley-Omar
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | - Diana Hardie
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | - Stephen Korsman
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | - Deelan Doolabh
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | - Wofgang Preiser
- National Health Laboratory Service, Cape Town, South Africa
- Division of Medical Virology, Stellenbosch University, Cape Town, South Africa
| | - Tongai Maponga
- National Health Laboratory Service, Cape Town, South Africa
- Division of Medical Virology, Stellenbosch University, Cape Town, South Africa
| | - Arash Iranzadeh
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | | | - Sean Wasserman
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Neshaad Schrueder
- Department of Medicine, Tygerberg Hospital,, Stellenbosch University, Cape Town, South Africa
| | - Linda Boloko
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Greg Symons
- Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Peter Raubenheimer
- Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Abraham Viljoen
- Department of Medicine, Tygerberg Hospital,, Stellenbosch University, Cape Town, South Africa
| | - Arifa Parker
- Department of Medicine, Tygerberg Hospital,, Stellenbosch University, Cape Town, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Waasila Jasat
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu Natal, Durban, South Africa
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- The Francis Crick Institute, London, UK
- Department of Infectious Diseases, Imperial College London, London, UK
| | - Andrew Boulle
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Marvin Hsiao
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
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4
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Davies MA, Morden E, Rosseau P, Arendse J, Bam JL, Boloko L, Cloete K, Cohen C, Chetty N, Dane P, Heekes A, Hsiao NY, Hunter M, Hussey H, Jacobs T, Jassat W, Kariem S, Kassanjee R, Laenen I, Le Roux S, Lessells R, Mahomed H, Maughan D, Meintjes G, Mendelson M, Mnguni A, Moodley M, Murie K, Naude J, Ntusi NAB, Paleker M, Parker A, Pienaar D, Preiser W, Prozesky H, Raubenheimer P, Rossouw L, Schrueder N, Smith B, Smith M, Solomon W, Symons G, Taljaard J, Wasserman S, Wilkinson RJ, Wolmarans M, Wolter N, Boulle A. Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa. medRxiv 2022:2022.06.28.22276983. [PMID: 35794899 PMCID: PMC9258293 DOI: 10.1101/2022.06.28.22276983] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Objective 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. Methods We included public sector patients aged ≥20 years with laboratory-confirmed COVID-19 between 1-21 May 2022 (BA.4/BA.5 wave) and equivalent prior wave periods. We compared the risk between waves of (i) death and (ii) severe hospitalization/death (all within 21 days of diagnosis) using Cox regression adjusted for demographics, comorbidities, admission pressure, vaccination and prior infection. Results Among 3,793 patients from the BA.4/BA.5 wave and 190,836 patients from previous waves the risk of severe hospitalization/death was similar in the BA.4/BA.5 and BA.1 waves (adjusted hazard ratio [aHR] 1.12; 95% confidence interval [CI] 0.93; 1.34). Both Omicron waves had lower risk of severe outcomes than previous waves. Prior infection (aHR 0.29, 95% CI 0.24; 0.36) and vaccination (aHR 0.17; 95% CI 0.07; 0.40 for boosted vs. no vaccine) were protective. Conclusion Disease severity was similar amongst diagnosed COVID-19 cases in the BA.4/BA.5 and BA.1 periods in the context of growing immunity against SARS-CoV-2 due to prior infection and vaccination, both of which were strongly protective.
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Affiliation(s)
- Mary-Ann Davies
- Health Intelligence, Western Cape Government: Health and Wellness, South Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | - Erna Morden
- Health Intelligence, Western Cape Government: Health and Wellness, South Africa
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | | | | | - Jamy-Lee Bam
- Health Intelligence, Western Cape Government: Health and Wellness, South Africa
| | - Linda Boloko
- Groote Schuur Hospital, Western Cape Government: Health and Wellness, South Africa
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, South Africa
| | - Keith Cloete
- Western Cape Government: Health and Wellness, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, National Health Laboratory Service, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Chetty
- Health Intelligence, Western Cape Government: Health and Wellness, South Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | - Pierre Dane
- Health Intelligence, Western Cape Government: Health and Wellness, South Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | - Alexa Heekes
- Health Intelligence, Western Cape Government: Health and Wellness, South Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | - Nei-Yuan Hsiao
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service, South Africa
| | - Mehreen Hunter
- Health Intelligence, Western Cape Government: Health and Wellness, South Africa
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | - Hannah Hussey
- Health Intelligence, Western Cape Government: Health and Wellness, South Africa
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, South Africa
- Metro Health Services, Western Cape Government: Health and Wellness
| | - Theuns Jacobs
- Health Intelligence, Western Cape Government: Health and Wellness, South Africa
| | - Waasila Jassat
- National Institute for Communicable Diseases, National Health Laboratory Service, South Africa
| | - Saadiq Kariem
- Western Cape Government: Health and Wellness, South Africa
| | - Reshma Kassanjee
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | - Inneke Laenen
- Health Intelligence, Western Cape Government: Health and Wellness, South Africa
- Division of Health Systems and Public Health, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University
| | - Sue Le Roux
- Western Cape Government: Health and Wellness, South Africa
- Karl Bremer Hospital, Western Cape Government: Health and Wellness
| | - Richard Lessells
- KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
| | - Hassan Mahomed
- Metro Health Services, Western Cape Government: Health and Wellness
- Division of Health Systems and Public Health, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University
| | - Deborah Maughan
- Groote Schuur Hospital, Western Cape Government: Health and Wellness, South Africa
- Department of Medicine, University of Cape Town, South Africa
| | - Graeme Meintjes
- Groote Schuur Hospital, Western Cape Government: Health and Wellness, South Africa
- Department of Medicine, University of Cape Town, South Africa
| | - Marc Mendelson
- Groote Schuur Hospital, Western Cape Government: Health and Wellness, South Africa
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, South Africa
| | - Ayanda Mnguni
- Khayelitsha District Hospital, Western Cape Government: Health and Wellness
| | - Melvin Moodley
- Health Intelligence, Western Cape Government: Health and Wellness, South Africa
| | - Katy Murie
- Western Cape Government: Health and Wellness, South Africa
- Metro Health Services, Western Cape Government: Health and Wellness
| | - Jonathan Naude
- Mitchells Plain Hospital, Western Cape Government: Health and Wellness
| | - Ntobeko A. B. Ntusi
- Groote Schuur Hospital, Western Cape Government: Health and Wellness, South Africa
- Department of Medicine, University of Cape Town, South Africa
- South African Medical Research Council Extramural Unit on Intersection of Noncommunicable Diseases and Infectious Diseases
| | - Masudah Paleker
- Health Intelligence, Western Cape Government: Health and Wellness, South Africa
- Division of Health Systems and Public Health, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University
| | - Arifa Parker
- Tygerberg Hospital, Western Cape Government: Health and Wellness
- Division of Infectious Diseases, Department of Medicine, Stellenbosch University, South Africa
| | - David Pienaar
- Rural Health Services, Western Cape Government: Health and Wellness
| | - Wolfgang Preiser
- National Health Laboratory Service, South Africa
- Division of Medical Virology, University of Stellenbosch, South Africa
| | - Hans Prozesky
- Tygerberg Hospital, Western Cape Government: Health and Wellness
- Division of Infectious Diseases, Department of Medicine, Stellenbosch University, South Africa
| | - Peter Raubenheimer
- Groote Schuur Hospital, Western Cape Government: Health and Wellness, South Africa
- Department of Medicine, University of Cape Town, South Africa
| | - Liezel Rossouw
- Western Cape Government: Health and Wellness, South Africa
| | - Neshaad Schrueder
- Tygerberg Hospital, Western Cape Government: Health and Wellness
- Division of General Medicine, Department of Medicine, Stellenbosch University, South Africa
| | - Barry Smith
- Western Cape Government: Health and Wellness, South Africa
- Karl Bremer Hospital, Western Cape Government: Health and Wellness
| | - Mariette Smith
- Health Intelligence, Western Cape Government: Health and Wellness, South Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | | | - Greg Symons
- Groote Schuur Hospital, Western Cape Government: Health and Wellness, South Africa
- Department of Medicine, University of Cape Town, South Africa
| | - Jantjie Taljaard
- Tygerberg Hospital, Western Cape Government: Health and Wellness
- Division of Infectious Diseases, Department of Medicine, Stellenbosch University, South Africa
| | - Sean Wasserman
- Groote Schuur Hospital, Western Cape Government: Health and Wellness, South Africa
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, South Africa
| | - Robert J. Wilkinson
- The Francis Crick Institute, Midland Road, London, NW1 1AT, UK
- Department of Infectious Diseases, Imperial College London, W12 0NN, UK
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | | | - Nicole Wolter
- National Institute for Communicable Diseases, National Health Laboratory Service, South Africa
- School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Andrew Boulle
- Health Intelligence, Western Cape Government: Health and Wellness, South Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, South Africa
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5
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Davies M, Kassanjee R, Rousseau P, Morden E, Johnson L, Solomon W, Hsiao N, Hussey H, Meintjes G, Paleker M, Jacobs T, Raubenheimer P, Heekes A, Dane P, Bam J, Smith M, Preiser W, Pienaar D, Mendelson M, Naude J, Schrueder N, Mnguni A, Le Roux S, Murie K, Prozesky H, Mahomed H, Rossouw L, Wasserman S, Maughan D, Boloko L, Smith B, Taljaard J, Symons G, Ntusi NAB, Parker A, Wolter N, Jassat W, Cohen C, Lessells R, Wilkinson RJ, Arendse J, Kariem S, Moodley M, Wolmarans M, Cloete K, Boulle A. 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. Trop Med Int Health 2022; 27:564-573. [PMID: 35411997 PMCID: PMC9115442 DOI: 10.1111/tmi.13752] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
OBJECTIVES 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. METHODS In this cohort study, we included public sector patients aged ≥20 years with a laboratory-confirmed COVID-19 diagnosis between 14 November and 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 hospitalisation or death and any hospitalisation or death (all ≤14 days after diagnosis) adjusted for age, sex, comorbidities, geography, vaccination and prior infection. RESULTS We included 5144 patients from wave four and 11,609 from prior waves. The 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 a modest reduction in risk of severe hospitalisation or death compared to the Delta-driven wave.
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Affiliation(s)
- Mary‐Ann Davies
- Health Intelligence, Western Cape Government: HealthCape TownSouth Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape TownCape TownSouth Africa
- Division of Public Health MedicineSchool of Public Health and Family Medicine, University of Cape TownCape TownSouth Africa
| | - Reshma Kassanjee
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape TownCape TownSouth Africa
| | | | - Erna Morden
- Health Intelligence, Western Cape Government: HealthCape TownSouth Africa
- Division of Public Health MedicineSchool of Public Health and Family Medicine, University of Cape TownCape TownSouth Africa
| | - Leigh Johnson
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape TownCape TownSouth Africa
| | | | - Nei‐Yuan Hsiao
- Division of Medical VirologyUniversity of Cape TownCape TownSouth Africa
- National Health Laboratory ServiceCape TownSouth Africa
| | - Hannah Hussey
- Health Intelligence, Western Cape Government: HealthCape TownSouth Africa
- Division of Public Health MedicineSchool of Public Health and Family Medicine, University of Cape TownCape TownSouth Africa
| | - Graeme Meintjes
- Groote Schuur Hospital, Western Cape Government: HealthCape TownSouth Africa
- Department of MedicineUniversity of Cape TownCape TownSouth Africa
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
| | - Masudah Paleker
- Health Intelligence, Western Cape Government: HealthCape TownSouth Africa
- Division of Health Systems and Public Health, Department of Global HealthStellenbosch UniversityTygerbergSouth Africa
| | - Theuns Jacobs
- Health Intelligence, Western Cape Government: HealthCape TownSouth Africa
| | - Peter Raubenheimer
- Groote Schuur Hospital, Western Cape Government: HealthCape TownSouth Africa
- Department of MedicineUniversity of Cape TownCape TownSouth Africa
| | - Alexa Heekes
- Health Intelligence, Western Cape Government: HealthCape TownSouth Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape TownCape TownSouth Africa
| | - Pierre Dane
- Health Intelligence, Western Cape Government: HealthCape TownSouth Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape TownCape TownSouth Africa
| | - Jamy‐Lee Bam
- Health Intelligence, Western Cape Government: HealthCape TownSouth Africa
| | - Mariette Smith
- Health Intelligence, Western Cape Government: HealthCape TownSouth Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape TownCape TownSouth Africa
| | - Wolfgang Preiser
- National Health Laboratory ServiceCape TownSouth Africa
- Division of Medical VirologyStellenbosch UniversityStellenboschSouth Africa
| | - David Pienaar
- Rural Health Services, Western Cape Government: HealthCape TownSouth Africa
| | - Marc Mendelson
- Groote Schuur Hospital, Western Cape Government: HealthCape TownSouth Africa
- Division of Infectious Diseases and HIV Medicine, Department of MedicineUniversity of Cape TownCape TownSouth Africa
| | - Jonathan Naude
- Mitchells Plain Hospital, Western Cape Government: HealthCape TownSouth Africa
| | - Neshaad Schrueder
- Tygerberg Hospital, Western Cape Government: HealthParowSouth Africa
- Department of MedicineStellenbosch UniversityStellenboschSouth Africa
| | - Ayanda Mnguni
- Khayelitsha District Hospital, Western Cape Government: HealthKhayelitshaSouth Africa
| | - Sue Le Roux
- Karl Bremer Hospital, Western Cape Government: HealthBellvilleSouth Africa
- Western Cape Government: HealthCape TownSouth Africa
| | - Kathleen Murie
- Western Cape Government: HealthCape TownSouth Africa
- Metro Health Services, Western Cape Government: HealthCape TownSouth Africa
| | - Hans Prozesky
- Tygerberg Hospital, Western Cape Government: HealthParowSouth Africa
- Division of Infectious Diseases, Department of MedicineStellenbosch UniversityTygerbergSouth Africa
| | - Hassan Mahomed
- Division of Health Systems and Public Health, Department of Global HealthStellenbosch UniversityTygerbergSouth Africa
- Metro Health Services, Western Cape Government: HealthCape TownSouth Africa
| | | | - Sean Wasserman
- Groote Schuur Hospital, Western Cape Government: HealthCape TownSouth Africa
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
- Division of Infectious Diseases and HIV Medicine, Department of MedicineUniversity of Cape TownCape TownSouth Africa
| | - Deborah Maughan
- Groote Schuur Hospital, Western Cape Government: HealthCape TownSouth Africa
- Department of MedicineUniversity of Cape TownCape TownSouth Africa
| | - Linda Boloko
- Groote Schuur Hospital, Western Cape Government: HealthCape TownSouth Africa
- Division of Infectious Diseases and HIV Medicine, Department of MedicineUniversity of Cape TownCape TownSouth Africa
| | - Barry Smith
- Karl Bremer Hospital, Western Cape Government: HealthBellvilleSouth Africa
- Western Cape Government: HealthCape TownSouth Africa
| | - Jantjie Taljaard
- Tygerberg Hospital, Western Cape Government: HealthParowSouth Africa
- Division of Infectious Diseases, Department of MedicineStellenbosch UniversityTygerbergSouth Africa
| | - Greg Symons
- Groote Schuur Hospital, Western Cape Government: HealthCape TownSouth Africa
- Department of MedicineUniversity of Cape TownCape TownSouth Africa
| | - Ntobeko A. B. Ntusi
- Groote Schuur Hospital, Western Cape Government: HealthCape TownSouth Africa
- Department of MedicineUniversity of Cape TownCape TownSouth Africa
| | - Arifa Parker
- Tygerberg Hospital, Western Cape Government: HealthParowSouth Africa
- Division of Infectious Diseases, Department of MedicineStellenbosch UniversityTygerbergSouth Africa
| | - Nicole Wolter
- National Institute for Communicable Diseases, National Health Laboratory ServiceJohannesburgSouth Africa
| | - Waasila Jassat
- National Institute for Communicable Diseases, National Health Laboratory ServiceJohannesburgSouth Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, National Health Laboratory ServiceJohannesburgSouth Africa
- Faculty of Health Sciences, School of Public Health, University of the WitwatersrandJohannesburgSouth Africa
| | - Richard Lessells
- KwaZulu‐Natal Research, Innovation & Sequencing Platform, University of KwaZulu‐NatalDurbanSouth Africa
| | - Robert J. Wilkinson
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
- Francis Crick InstituteLondonUK
- Department of Infectious DiseasesImperial College LondonLondonUK
| | | | - Saadiq Kariem
- Western Cape Government: HealthCape TownSouth Africa
| | - Melvin Moodley
- Health Intelligence, Western Cape Government: HealthCape TownSouth Africa
| | | | - Keith Cloete
- Western Cape Government: HealthCape TownSouth Africa
| | - Andrew Boulle
- Health Intelligence, Western Cape Government: HealthCape TownSouth Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape TownCape TownSouth Africa
- Division of Public Health MedicineSchool of Public Health and Family Medicine, University of Cape TownCape TownSouth Africa
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Hussey H, Davies MA, 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 RJ, Boulle A, Hsiao NY. 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. Int J Infect Dis 2022; 118:150-154. [PMID: 35235826 PMCID: PMC8882068 DOI: 10.1016/j.ijid.2022.02.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/08/2022] [Accepted: 02/23/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND 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. 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 November 1 to December 14, 2021 in the Western Cape Province, South Africa, in the public sector. Adjustments were made for vaccination status and prior diagnosis of infection. RESULTS A total of 150 cases with RTD and 1486 cases without RTD were included. Cases without RTD had a lower hazard of admission (adjusted hazard ratio [aHR], 0.56; 95% confidence interval [CI], 0.34-0.91). Complete vaccination was protective against 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 with 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.
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Affiliation(s)
- Hannah Hussey
- Health Intelligence, Western Cape Government: Health, South Africa; Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, South Africa.
| | - Mary-Ann Davies
- Health Intelligence, Western Cape Government: Health, South Africa; Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | - Alexa Heekes
- Health Intelligence, Western Cape Government: Health, South Africa; Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | - Carolyn Williamson
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa; Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - Ziyaad Valley-Omar
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
| | - Diana Hardie
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
| | - Stephen Korsman
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
| | - Deelan Doolabh
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
| | - Wolfgang Preiser
- National Health Laboratory Service, South Africa; Division of Medical Virology, University of Stellenbosch, South Africa
| | - Tongai Maponga
- National Health Laboratory Service, South Africa; Division of Medical Virology, University of Stellenbosch, South Africa
| | - Arash Iranzadeh
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
| | - Sean Wasserman
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, South Africa
| | - Linda Boloko
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Department of Medicine, Groote Schuur Hospital, University of Cape Town, South Africa
| | - Greg Symons
- Department of Medicine, Groote Schuur Hospital, University of Cape Town, South Africa
| | - Peter Raubenheimer
- Department of Medicine, Groote Schuur Hospital, University of Cape Town, South Africa
| | - Arifa Parker
- Department of Medicine, Tygerberg Hospital, Stellenbosch University, South Africa
| | - Neshaad Schrueder
- Department of Medicine, Tygerberg Hospital, Stellenbosch University, South Africa
| | | | | | - Nicole Wolter
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Waasila Jassat
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; The Francis Crick Institute, Midland Road, London, NW1 1AT, UK; Department of Infectious Diseases, Imperial College London, W12 0NN, UK
| | - Andrew Boulle
- Health Intelligence, Western Cape Government: Health, South Africa; Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | - Nei-Yuan Hsiao
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa; Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
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7
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Davies MA, Kassanjee R, Rosseau P, Morden E, Johnson L, Solomon W, Hsiao NY, Hussey H, Meintjes G, Paleker M, Jacobs T, Raubenheimer P, Heekes A, Dane P, Bam JL, Smith M, Preiser W, Pienaar D, Mendelson M, Naude J, Schrueder N, Mnguni A, Roux SL, Murie K, Prozesky H, Mahomed H, Rossouw L, Wasserman S, Maughan D, Boloko L, Smith B, Taljaard J, Symons G, Ntusi N, Parker A, Wolter N, Jassat W, Cohen C, Lessells R, Wilkinson RJ, Arendse J, Kariem S, Moodley M, Vallabhjee K, Wolmarans M, Cloete K, Boulle A. 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. medRxiv 2022:2022.01.12.22269148. [PMID: 35043121 PMCID: PMC8764730 DOI: 10.1101/2022.01.12.22269148] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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.
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Affiliation(s)
- Mary-Ann Davies
- Health Intelligence, Western Cape Government: Health, South Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town
| | - Reshma Kassanjee
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | | | - Erna Morden
- Health Intelligence, Western Cape Government: Health, South Africa
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town
| | - Leigh Johnson
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | | | - Nei-Yuan Hsiao
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service, South Africa
| | - Hannah Hussey
- Health Intelligence, Western Cape Government: Health, South Africa
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town
| | - Graeme Meintjes
- Groote Schuur Hospital, Western Cape Government: Health
- Department of Medicine, University of Cape Town
| | - Masudah Paleker
- Health Intelligence, Western Cape Government: Health, South Africa
- Division of Health Systems and Public Health, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University
| | - Theuns Jacobs
- Health Intelligence, Western Cape Government: Health, South Africa
| | - Peter Raubenheimer
- Groote Schuur Hospital, Western Cape Government: Health
- Department of Medicine, University of Cape Town
| | - Alexa Heekes
- Health Intelligence, Western Cape Government: Health, South Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | - Pierre Dane
- Health Intelligence, Western Cape Government: Health, South Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | - Jamy-Lee Bam
- Health Intelligence, Western Cape Government: Health, South Africa
| | - Mariette Smith
- Health Intelligence, Western Cape Government: Health, South Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | - Wolfgang Preiser
- National Health Laboratory Service, South Africa
- Division of Medical Virology, University of Stellenbosch, South Africa
| | - David Pienaar
- Rural Health Services, Western Cape Government: Health
| | - Marc Mendelson
- Groote Schuur Hospital, Western Cape Government: Health
- Department of Medicine, University of Cape Town
| | - Jonathan Naude
- Mitchells Plain Hospital, Western Cape Government: Health
| | - Neshaad Schrueder
- Tygerberg Hospital, Western Cape Government: Health
- Department of Medicine, Stellenbosch University, South Africa
| | - Ayanda Mnguni
- Khayelitsha District Hospital, Western Cape Government: Health
| | - Sue Le Roux
- Groote Schuur Hospital, Western Cape Government: Health
- Department of Medicine, University of Cape Town
| | - Katie Murie
- Western Cape Government: Health, South Africa
| | - Hans Prozesky
- Tygerberg Hospital, Western Cape Government: Health
- Department of Medicine, Stellenbosch University, South Africa
| | - Hassan Mahomed
- Division of Health Systems and Public Health, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University
- Metro Health Services, Western Cape Government: Health
| | | | - Sean Wasserman
- Groote Schuur Hospital, Western Cape Government: Health
- Department of Medicine, University of Cape Town
| | - Deborah Maughan
- Groote Schuur Hospital, Western Cape Government: Health
- Department of Medicine, University of Cape Town
| | - Linda Boloko
- Groote Schuur Hospital, Western Cape Government: Health
- Department of Medicine, University of Cape Town
| | - Barry Smith
- Groote Schuur Hospital, Western Cape Government: Health
- Department of Medicine, University of Cape Town
| | - Jantjie Taljaard
- Tygerberg Hospital, Western Cape Government: Health
- Department of Medicine, Stellenbosch University, South Africa
| | - Greg Symons
- Groote Schuur Hospital, Western Cape Government: Health
- Department of Medicine, University of Cape Town
| | - Ntobeko Ntusi
- Groote Schuur Hospital, Western Cape Government: Health
- Department of Medicine, University of Cape Town
| | - Arifa Parker
- Tygerberg Hospital, Western Cape Government: Health
- Department of Medicine, Stellenbosch University, South Africa
| | - Nicole Wolter
- National Institute for Communicable Diseases, National Health Laboratory Service, South Africa
| | - Waasila Jassat
- National Institute for Communicable Diseases, National Health Laboratory Service, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, National Health Laboratory Service, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
| | - Robert J Wilkinson
- The Francis Crick Institute, Midland Road, London, NW1 1AT, UK
- Department of Infectious Diseases, Imperial College London, W12 0NN, UK
| | | | | | - Melvin Moodley
- Health Intelligence, Western Cape Government: Health, South Africa
| | | | | | | | - Andrew Boulle
- Health Intelligence, Western Cape Government: Health, South Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town
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Calligaro GL, Moodley L, Symons G, Dheda K. The medical and surgical treatment of drug-resistant tuberculosis. J Thorac Dis 2014; 6:186-95. [PMID: 24624282 PMCID: PMC3949182 DOI: 10.3978/j.issn.2072-1439.2013.11.11] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 11/20/2013] [Indexed: 11/14/2022]
Abstract
Multi drug-resistant tuberculosis (MDR-TB) and extensively drug-resistant TB (XDR-TB) are burgeoning global problems with high mortality which threaten to destabilise TB control programs in several parts of the world. Of alarming concern is the emergence, in large numbers, of patients with resistance beyond XDR-TB (totally drug-resistant TB; TDR-TB or extremely drug resistant TB; XXDR-TB). Given the burgeoning global phenomenon of MDR-TB, XDR-TB and TDR-TB, and increasing international migration and travel, healthcare workers, researchers, and policy makers in TB endemic and non-endemic countries should familiarise themselves with issues relevant to the management of these patients. Given the lack of novel TB drugs and limited access to existing drugs such as linezolid and bedaquiline in TB endemic countries, significant numbers of therapeutic failures are emerging from the ranks of those with XDR-TB. Given the lack of appropriate facilities in resource-limited settings, such patients are being discharged back into the community where there is likely ongoing disease spread. In the absence of effective drug regimens, in appropriate patients, surgery is a critical part of management. Here we review the diagnosis, medical and surgical management of MDR-TB and XDR-TB.
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Shean K, Streicher E, Pieterson E, Symons G, van Zyl Smit R, Theron G, Lehloenya R, Padanilam X, Wilcox P, Victor TC, van Helden P, Groubusch M, Warren R, Badri M, Dheda K. Drug-associated adverse events and their relationship with outcomes in patients receiving treatment for extensively drug-resistant tuberculosis in South Africa. PLoS One 2013; 8:e63057. [PMID: 23667572 PMCID: PMC3646906 DOI: 10.1371/journal.pone.0063057] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 03/31/2013] [Indexed: 01/08/2023] Open
Abstract
Background Treatment-related outcomes in patients with extensively drug-resistant tuberculosis (XDR-TB) are poor. However, data about the type, frequency and severity of presumed drug-associated adverse events (AEs) and their association with treatment-related outcomes in patients with XDR-TB are scarce. Methods Case records of 115 South-African XDR-TB patients were retrospectively reviewed by a trained researcher. AEs were estimated and graded according to severity [grade 0 = none; grade 1–2 = mild to moderate; and grade 3–5 = severe (drug stopped, life-threatening or death)]. Findings 161 AEs were experienced by 67/115(58%) patients: 23/67(34%) required modification of treatment, the offending drug was discontinued in 19/67(28%), reactions were life-threatening in 2/67(3.0%), and 6/67(9.0%) died. ∼50% of the patients were still on treatment at the time of data capture. Sputum culture-conversion was less likely in those with severe (grade 3–5) vs. grade 0–2 AEs [2/27(7%) vs. 24/88(27%); p = 0.02]. The type, frequency and severity of AEs was similar in HIV-infected and uninfected patients. Capreomycin, which was empirically administered in most cases, was withdrawn in 14/104(14%) patients, implicated in (14/34) 41% of the total drug withdrawals, and was associated with all 6 deaths in the severe AE group (renal failure in five patients and hypokalemia in one patient). Conclusion Drug-associated AEs occur commonly with XDR-TB treatment, are often severe, frequently interrupt therapy, and negatively impact on culture conversion outcomes. These preliminary data inform on the need for standardised strategies (including pre-treatment counselling, early detection, monitoring, and follow-up) and less toxic drugs to optimally manage patients with XDR-TB.
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Affiliation(s)
- Karen Shean
- Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Elizabeth Streicher
- DST/NRF Centre of Excellence for Biomedical TB Research/MRC Centre for Molecular and Cellular Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Elize Pieterson
- Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Greg Symons
- Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Richard van Zyl Smit
- Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Grant Theron
- Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Rannakoe Lehloenya
- Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Xavier Padanilam
- Sizwe Tropical Diseases Hospital, Sandringham, Johannesburg, South Africa
- Division of Infectious Diseases, Department of Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Paul Wilcox
- Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Tommie C. Victor
- DST/NRF Centre of Excellence for Biomedical TB Research/MRC Centre for Molecular and Cellular Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Paul van Helden
- DST/NRF Centre of Excellence for Biomedical TB Research/MRC Centre for Molecular and Cellular Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Martin Groubusch
- Sizwe Tropical Diseases Hospital, Sandringham, Johannesburg, South Africa
- National Health Laboratory Service and Division of Clinical Microbiology and Infectious Diseases, University of Witwatersrand, Johannesburg, South Africa
- Division of Infectious Diseases, Department of Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Center for Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Division of Internal Medicine, Amsterdam Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Robin Warren
- DST/NRF Centre of Excellence for Biomedical TB Research/MRC Centre for Molecular and Cellular Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Motasim Badri
- Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Keertan Dheda
- Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Infection, University College London Medical School, London, United Kingdom
- * E-mail:
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Dheda K, van Zyl-Smit RN, Meldau R, Meldau S, Symons G, Khalfey H, Govender N, Rosu V, Sechi LA, Maredza A, Semple P, Whitelaw A, Wainwright H, Badri M, Dawson R, Bateman ED, Zumla A. Quantitative lung T cell responses aid the rapid diagnosis of pulmonary tuberculosis. Thorax 2009; 64:847-53. [DOI: 10.1136/thx.2009.116376] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Dheda K, van Zyl-Smit RN, Sechi LA, Badri M, Meldau R, Meldau S, Symons G, Semple PL, Maredza A, Dawson R, Wainwright H, Whitelaw A, Vallie Y, Raubenheimer P, Bateman ED, Zumla A. Utility of quantitative T-cell responses versus unstimulated interferon- for the diagnosis of pleural tuberculosis. Eur Respir J 2009; 34:1118-26. [DOI: 10.1183/09031936.00005309] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Symons G, Jager C, Ross J, Reid J. Do brassinosteroids undergo long-distance transport in plants? Comp Biochem Physiol A Mol Integr Physiol 2007. [DOI: 10.1016/j.cbpa.2007.01.542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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