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Sikhosana ML, Welch R, Musekiwa A, Makatini Z, Ebonwu J, Blumberg L, Jassat W. Association between SARS-CoV-2 gene specific Ct values and COVID-19 associated in-hospital mortality. Front Epidemiol 2024; 4:1375975. [PMID: 38737987 PMCID: PMC11082284 DOI: 10.3389/fepid.2024.1375975] [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] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/08/2024] [Indexed: 05/14/2024]
Abstract
Background Since there are currently no specific SARS-CoV-2 prognostic viral biomarkers for predicting disease severity, there has been interest in using SARS-CoV-2 polymerase chain reaction (PCR) cycle-threshold (Ct) values to predict disease progression. Objective This study assessed the association between in-hospital mortality of hospitalized COVID-19 cases and Ct-values of gene targets specific to SARS-CoV-2. Methods Clinical data of hospitalized COVID-19 cases from Gauteng Province from April 2020-July 2022 were obtained from a national surveillance system and linked to laboratory data. The study period was divided into pandemic waves: Asp614Gly/wave1 (7 June-22 Aug 2020); beta/wave2 (15 Nov 2020-6 Feb 2021); delta/wave3 (9 May-18 Sept 2021) and omicron/wave4 (21 Nov 2021-22 Jan 2022). Ct-value data of genes specific to SARS-CoV-2 according to testing platforms (Roche-ORF gene; GeneXpert-N2 gene; Abbott-RdRp gene) were categorized as low (Ct < 20), mid (Ct20-30) or high (Ct > 30). Results There were 1205 recorded cases: 836(69.4%; wave1), 122(10.1%;wave2) 21(1.7%; wave3) and 11(0.9%;in wave4). The cases' mean age(±SD) was 49 years(±18), and 662(54.9%) were female. There were 296(24.6%) deaths recorded: 241(81.4%;wave1), 27 (9.1%;wave2), 6 (2%;wave3), and 2 (0.7%;wave4) (p < 0.001). Sample distribution by testing platforms was: Roche 1,033 (85.7%), GeneXpert 169 (14%) and Abbott 3 (0.3%). The median (IQR) Ct-values according to testing platform were: Roche 26 (22-30), GeneXpert 38 (36-40) and Abbott 21 (16-24). After adjusting for sex, age and presence of a comorbidity, the odds of COVID-19 associated death were high amongst patients with Ct values 20-30[adjusted Odds Ratio (aOR) 2.25; 95% CI: 1.60-3.18] and highest amongst cases with Ct-values <20 (aOR 3.18; 95% CI: 1.92-5.27), compared to cases with Ct-values >30. Conclusion Although odds of COVID19-related death were high amongst cases with Ct-values <30, Ct values were not comparable across different testing platforms, thus precluding the comparison of SARS-CoV-2 Ct-value results.
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Affiliation(s)
- Mpho L. Sikhosana
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- Department of Virology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Richard Welch
- Department of Public Health and Outbreak Response, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Alfred Musekiwa
- Faculty of Health Sciences, School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Zinhle Makatini
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- Department of Virology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Joy Ebonwu
- Department of Public Health and Outbreak Response, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Lucille Blumberg
- Department of Public Health and Outbreak Response, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Waasila Jassat
- Department of Public Health and Outbreak Response, National Institute for Communicable Diseases, Johannesburg, South Africa
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Jassat W, Mudara C, Ozougwu L, Welch R, Arendse T, Masha M, Blumberg L, Kufa T, Puren A, Groome M, Govender N, Pisa P, Govender S, Sanne I, Brahmbhatt H, Parmley L, Wolmarans M, Rousseau P, Selikow A, Burgess M, Hankel L, Parker A, Cohen C. Trends in COVID-19 admissions and deaths among people living with HIV in South Africa: analysis of national surveillance data. Lancet HIV 2024; 11:e96-e105. [PMID: 38296365 DOI: 10.1016/s2352-3018(23)00266-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 10/02/2023] [Accepted: 10/13/2023] [Indexed: 02/08/2024]
Abstract
BACKGROUND In 2021, the HIV prevalence among South African adults was 18% and more than 2 million people had uncontrolled HIV and, therefore, had increased risk of poor outcomes with SARS-CoV-2 infection. We investigated trends in COVID-19 admissions and factors associated with in-hospital COVID-19 mortality among people living with HIV and people without HIV. METHODS In this analysis of national surveillance data, we linked and analysed data collected between March 5, 2020, and May 28, 2022, from the DATCOV South African national COVID-19 hospital surveillance system, the SARS-CoV-2 case line list, and the Electronic Vaccination Data System. All analyses included patients hospitalised with SARS-CoV-2 with known in-hospital outcomes (ie, who were discharged alive or had died) at the time of data extraction. We used descriptive statistics for admissions and mortality trends. Using post-imputation random-effect multivariable logistic regression models, we compared characteristics and the case fatality ratio of people with HIV and people without HIV. Using modified Poisson regression models, we compared factors associated with mortality among all people with COVID-19 admitted to hospital and factors associated with mortality among people with HIV. FINDINGS Among 397 082 people with COVID-19 admitted to hospital, 301 407 (75·9%) were discharged alive, 89 565 (22·6%) died, and 6110 (1·5%) had no recorded outcome. 270 737 (68·2%) people with COVID-19 had documented HIV status (22 858 with HIV and 247 879 without). Comparing characteristics of people without HIV and people with HIV in each COVID-19 wave, people with HIV had increased odds of mortality in the D614G (adjusted odds ratio 1·19, 95% CI 1·09-1·29), beta (1·08, 1·01-1·16), delta (1·10, 1·03-1·18), omicron BA.1 and BA.2 (1·71, 1·54-1·90), and omicron BA.4 and BA.5 (1·81, 1·41-2·33) waves. Among all COVID-19 admissions, mortality was lower among people with previous SARS-CoV-2 infection (adjusted incident rate ratio 0·32, 95% CI 0·29-0·34) and with partial (0·93, 0·90-0·96), full (0·70, 0·67-0·73), or boosted (0·50, 0·41-0·62) COVID-19 vaccination. Compared with people without HIV who were unvaccinated, people without HIV who were vaccinated had lower risk of mortality (0·68, 0·65-0·71) but people with HIV who were vaccinated did not have any difference in mortality risk (1·08, 0·96-1·23). In-hospital mortality was higher for people with HIV with CD4 counts less than 200 cells per μL, irrespective of viral load and vaccination status. INTERPRETATION HIV and immunosuppression might be important risk factors for mortality as COVID-19 becomes endemic. FUNDING South African National Institute for Communicable Diseases, the South African National Government, and the United States Agency for International Development.
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Affiliation(s)
- Waasila Jassat
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; Right to Care, Pretoria, South Africa.
| | - Caroline Mudara
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Lovelyn Ozougwu
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; Right to Care, Pretoria, South Africa
| | - Richard Welch
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; Right to Care, Pretoria, South Africa
| | - Tracy Arendse
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; Right to Care, Pretoria, South Africa
| | - Maureen Masha
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; Right to Care, Pretoria, South Africa
| | - Lucille Blumberg
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; Right to Care, Pretoria, South Africa
| | - Tendesayi Kufa
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Adrian Puren
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Michelle Groome
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Nevashan Govender
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Pedro Pisa
- Right to Care, Pretoria, South Africa; Department of Human Nutrition and Dietetics, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | | | - Ian Sanne
- Right to Care, Pretoria, South Africa; School of Pathology (M Groome), Clinical HIV Research Unit, Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Heena Brahmbhatt
- United States Agency for International Development, Pretoria, South Africa; Department of Population, Family and Reproductive Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Lauren Parmley
- United States Agency for International Development, Pretoria, South Africa
| | | | | | - Anthony Selikow
- Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Melissa Burgess
- Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Lauren Hankel
- Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Arifa Parker
- Tygerberg Hospital and Division of Infectious Disease, University of Stellenbosch, Cape Town, South Africa
| | - Cheryl Cohen
- Division of Public Health Surveillance and Response, 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
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Kassanjee R, Davies MA, Heekes A, Mahomed H, Hawkridge AJ, Wolmarans M, Morden E, Jacobs T, Cohen C, Moultrie H, Lessells RJ, Van Der Walt N, Arendse JO, Goeiman H, Mudaly V, Wolter N, Walaza S, Jassat W, von Gottberg A, Hannan PL, Rousseau P, Feikin D, Cloete K, Boulle A. COVID-19 vaccine uptake and effectiveness by time since vaccination in the Western Cape province, South Africa: An observational cohort study during 2020-2022. medRxiv 2024:2024.01.24.24301721. [PMID: 38343866 PMCID: PMC10854330 DOI: 10.1101/2024.01.24.24301721] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
Background There are few data on the real-world effectiveness of COVID-19 vaccines and boosting in Africa, which experienced high levels of SARS-CoV-2 infection in a mostly vaccine-naïve population, and has limited vaccine coverage and competing health service priorities. We assessed the association between vaccination and severe COVID-19 in the Western Cape, South Africa. Methods We performed an observational cohort study of >2 million adults during 2020-2022. We described SARS-CoV-2 testing, COVID-19 outcomes, and vaccine uptake over time. We used multivariable cox models to estimate the association of BNT162b2 and Ad26.COV2.S vaccination with COVID-19-related hospitalisation and death, adjusting for demographic characteristics, underlying health conditions, socioeconomic status proxies and healthcare utilisation. Results By end 2022, only 41% of surviving adults had completed vaccination and 8% a booster dose, despite several waves of severe COVID-19. Recent vaccination was associated with notable reductions in severe COVID-19 during distinct analysis periods dominated by Delta, Omicron BA.1/2 and BA.4/5 (sub)lineages: within 6 months of completing vaccination or boosting, vaccine effectiveness was 46-92% for death (range across periods), 45-92% for admission with severe disease or death, and 25-90% for any admission or death. During the Omicron BA.4/5 wave, within 3 months of vaccination or boosting, BNT162b2 and Ad26.COV2.S were each 84% effective against death (95% CIs: 57-94 and 49-95, respectively). However, there were distinct reductions of VE at larger times post completing or boosting vaccination. Conclusions Continued emphasis on regular COVID-19 vaccination including boosting is important for those at high risk of severe COVID-19 even in settings with widespread infection-induced immunity.
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Affiliation(s)
- Reshma Kassanjee
- Centre for Infectious Disease Epidemiology and Research, School of Public Health, University of Cape Town, South Africa
| | - Mary-Ann Davies
- Centre for Infectious Disease Epidemiology and Research, School of Public Health, University of Cape Town, South Africa
- Division of Public Health Medicine, School of Public Health, University of Cape Town, South Africa
- Centre for Infectious Diseases Research in Africa, University of Cape Town, South Africa
- Health Intelligence, Western Cape Government Department of Health and Wellness, South Africa
| | - Alexa Heekes
- Centre for Infectious Disease Epidemiology and Research, School of Public Health, University of Cape Town, South Africa
- Health Intelligence, Western Cape Government Department of Health and Wellness, South Africa
| | - Hassan Mahomed
- Division of Health Systems and Public Health, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
- Metro Health Services, Western Cape Government Department of Health and Wellness, South Africa
| | - Anthony J Hawkridge
- Rural Health Services, Western Cape Government Department of Health and Wellness, South Africa
| | | | - Erna Morden
- Health Intelligence, Western Cape Government Department of Health and Wellness, South Africa
- School of Public Health, University of Cape Town, South Africa
| | - Theuns Jacobs
- Health Intelligence, Western Cape Government Department of Health and Wellness, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, South Africa
- School of Public Health, University of the Witwatersrand, South Africa
| | - Harry Moultrie
- Centre for Tuberculosis, National Institute for Communicable Diseases of the National Health Laboratory Service, South Africa
| | - Richard J Lessells
- KwaZulu-Natal Research Innovation & Sequencing Platform, University of KwaZulu-Natal, South Africa
| | - Nicolette Van Der Walt
- Emergency & Clinical Services Support, Western Cape Government Department of Health and Wellness, South Africa
| | - Juanita O Arendse
- Division of Health Systems and Public Health, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
- Emergency & Clinical Services Support, Western Cape Government Department of Health and Wellness, South Africa
| | - Hilary Goeiman
- Western Cape Government Department of Health and Wellness, South Africa
| | - Vanessa Mudaly
- Division of Public Health Medicine, School of Public Health, University of Cape Town, South Africa
- Western Cape Government Department of Health and Wellness, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, South Africa
- School of Pathology, University of the Witwatersrand, South Africa
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, South Africa
- School of Public Health, University of the Witwatersrand, South Africa
| | - Waasila Jassat
- Health Practice, Genesis Analytics, South Africa
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, South Africa
- School of Pathology, University of the Witwatersrand, South Africa
| | - Patrick L Hannan
- Division of Epidemiology and Biostatistics, School of Public Health, University of Cape Town, South Africa
| | - Petro Rousseau
- South African National Department of Health, South Africa
| | - Daniel Feikin
- Department of Immunizations, Vaccines, and Biologicals, World Health Organization, Switzerland
| | - Keith Cloete
- Western Cape Government Department of Health and Wellness, South Africa
| | - Andrew Boulle
- Centre for Infectious Disease Epidemiology and Research, School of Public Health, University of Cape Town, South Africa
- Division of Public Health Medicine, School of Public Health, University of Cape Town, South Africa
- Centre for Infectious Diseases Research in Africa, University of Cape Town, South Africa
- Health Intelligence, Western Cape Government Department of Health and Wellness, South Africa
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Dickson L, Le Roux SR, Mitrani L, Hill J, Jassat W, Cox H, Mlisana K, Black J, Loveday M, Grant A, Kielmann K, Ndjeka N, Moshabela M, Nicol M. Organisation of care for people receiving drug-resistant tuberculosis treatment in South Africa: a mixed methods study. BMJ Open 2023; 13:e067121. [PMID: 37977868 PMCID: PMC10660906 DOI: 10.1136/bmjopen-2022-067121] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023] Open
Abstract
OBJECTIVES Treatment for multidrug-resistant/rifampicin-resistant tuberculosis (MDR/RR-TB) is increasingly transitioning from hospital-centred to community-based care. A national policy for decentralised programmatic MDR/RR-TB care was adopted in South Africa in 2011. We explored variations in the implementation of care models in response to this change in policy, and the implications of these variations for people affected by MDR/RR-TB. DESIGN A mixed methods study was done of patient movements between healthcare facilities, reconstructed from laboratory records. Facility visits and staff interviews were used to determine reasons for movements. PARTICIPANTS AND SETTING People identified with MDR/RR-TB from 13 high-burden districts within South Africa. OUTCOME MEASURES Geospatial movement patterns were used to identify organisational models. Reasons for patient movement and implications of different organisational models for people affected by MDR/RR-TB and the health system were determined. RESULTS Among 191 participants, six dominant geospatial movement patterns were identified, which varied in average hospital stay (0-281 days), average patient distance travelled (12-198 km) and number of health facilities involved in care (1-5 facilities). More centralised models were associated with longer delays to treatment initiation and lengthy hospitalisation. Decentralised models facilitated family-centred care and were associated with reduced time to treatment and hospitalisation duration. Responsiveness to the needs of people affected by MDR/RR-TB and health system constraints was achieved through implementation of flexible models, or the implementation of multiple models in a district. CONCLUSIONS Understanding how models for organising care have evolved may assist policy implementers to tailor implementation to promote particular patterns of care organisation or encourage flexibility, based on patient needs and local health system resources. Our approach can contribute towards the development of a health systems typology for understanding how policy-driven models of service delivery are implemented in the context of variable resources.
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Affiliation(s)
- Lindy Dickson
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Sacha Roxanne Le Roux
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Leila Mitrani
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Jeremy Hill
- TB Centre, London School of Hygiene &Tropical Medicine, London, UK
| | - Waasila Jassat
- School of Public Health, University of the Western Cape, Bellville, South Africa
| | - Helen Cox
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Institute for Infectious Disease and Molecular Medicine and Wellcome Centre for Infectious Disease Research, University of Cape Town, Cape Town, South Africa
| | - Koleka Mlisana
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal College of Health Sciences, Durban, KwaZulu-Natal, South Africa
| | - John Black
- Division of Infectious Diseases, University of Cape Town, Cape Town, South Africa
| | - Marian Loveday
- South African Medical Research Council, Durban, South Africa
| | - Alison Grant
- TB Centre, London School of Hygiene &Tropical Medicine, London, UK
- Africa Health Research Institute, Somkhele, South Africa
| | - Karina Kielmann
- Institute of Tropical Medicine, Antwerp, Belgium
- Institute for Global Health and Development, Queen Margaret University, Edinburgh, UK
| | - Norbert Ndjeka
- National Tuberculosis Control Programme, National Department of Health, Pretoria, South Africa
- School of Nursing and Public Health, University of KwaZulu-Natal College of Health Sciences, Durban, KwaZulu-Natal, South Africa
| | - Mosa Moshabela
- School of Nursing and Public Health, University of KwaZulu-Natal College of Health Sciences, Durban, KwaZulu-Natal, South Africa
| | - Mark Nicol
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Marshall Centre for Infectious DIsease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
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5
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Gonçalves BP, Jassat W, Baruch J, Hashmi M, Rojek A, Dasgupta A, Martin-Loeches I, Reyes LF, Piubelli C, Citarella BW, Kartsonaki C, Lefèvre B, López Revilla JW, Lunn M, Harrison EM, Kraemer MUG, Shrapnel S, Horby P, Bisoffi Z, Olliaro PL, Merson L. A multi-country analysis of COVID-19 hospitalizations by vaccination status. Med 2023; 4:797-812.e2. [PMID: 37738979 PMCID: PMC10935543 DOI: 10.1016/j.medj.2023.08.005] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/18/2023] [Accepted: 08/25/2023] [Indexed: 09/24/2023]
Abstract
BACKGROUND Individuals vaccinated against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), when infected, can still develop disease that requires hospitalization. It remains unclear whether these patients differ from hospitalized unvaccinated patients with regard to presentation, coexisting comorbidities, and outcomes. METHODS Here, we use data from an international consortium to study this question and assess whether differences between these groups are context specific. Data from 83,163 hospitalized COVID-19 patients (34,843 vaccinated, 48,320 unvaccinated) from 38 countries were analyzed. FINDINGS While typical symptoms were more often reported in unvaccinated patients, comorbidities, including some associated with worse prognosis in previous studies, were more common in vaccinated patients. Considerable between-country variation in both in-hospital fatality risk and vaccinated-versus-unvaccinated difference in this outcome was observed. CONCLUSIONS These findings will inform allocation of healthcare resources in future surges as well as design of longer-term international studies to characterize changes in clinical profile of hospitalized COVID-19 patients related to vaccination history. FUNDING This work was made possible by the UK Foreign, Commonwealth and Development Office and Wellcome (215091/Z/18/Z, 222410/Z/21/Z, 225288/Z/22/Z, and 220757/Z/20/Z); the Bill & Melinda Gates Foundation (OPP1209135); and the philanthropic support of the donors to the University of Oxford's COVID-19 Research Response Fund (0009109). Additional funders are listed in the "acknowledgments" section.
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Affiliation(s)
| | - Waasila Jassat
- National Institute for Communicable Diseases, Johannesburg, South Africa; Right to Care, Pretoria, South Africa
| | - Joaquín Baruch
- ISARIC, Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Madiha Hashmi
- Critical Care Asia and Ziauddin University, Karachi, Pakistan
| | - Amanda Rojek
- ISARIC, Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Abhishek Dasgupta
- Doctoral Training Centre, University of Oxford, Oxford, UK; Department of Biology, University of Oxford, Oxford, UK
| | - Ignacio Martin-Loeches
- Department of Intensive Care Medicine, Multidisciplinary Intensive Care Research Organization (MICRO), St James's Hospital, Leinster, Dublin, Ireland; Pulmonary Intensive Care Unit, Respiratory Institute, Hospital Clinic of Barcelona, IDIBAPS (Institut d'Investigacions Biomèdiques August Pi i Sunyer), University of Barcelona, CIBERes, Barcelona, Spain
| | - Luis Felipe Reyes
- Unisabana Center for Translational Science, School of Medicine, Universidad de La Sabana, Chía, Colombia
| | - Chiara Piubelli
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
| | | | - Christiana Kartsonaki
- MRC Population Health Research Unit, Clinical Trials Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Benjamin Lefèvre
- Université de Lorraine, CHRU-Nancy, Service des Maladies Infectieuses et Tropicales, Nancy, France; Université de Lorraine, APEMAC, Nancy, France
| | - José W López Revilla
- Instituto Nacional del Niño San Borja and Facultad de Ciencias de la Salud, Universidad Científica del Sur, Lima, Peru
| | - Miles Lunn
- ISARIC, Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Ewen M Harrison
- Centre for Medical Informatics, The University of Edinburgh, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Moritz U G Kraemer
- Department of Biology, University of Oxford, Oxford, UK; Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Sally Shrapnel
- Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane, Australia; School of Mathematics and Physics, Faculty of Science, The University of Queensland, St Lucia, Brisbane, Australia
| | - Peter Horby
- ISARIC, Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Zeno Bisoffi
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
| | - Piero L Olliaro
- ISARIC, Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Laura Merson
- ISARIC, Pandemic Sciences Institute, University of Oxford, Oxford, UK
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Zhu Y, Almeida FJ, Baillie JK, Bowen AC, Britton PN, Brizuela ME, Buonsenso D, Burgner D, Chew KY, Chokephaibulkit K, Cohen C, Cormier SA, Crawford N, Curtis N, Farias CGA, Gilks CF, von Gottberg A, Hamer D, Jarovsky D, Jassat W, Jesus AR, Kemp LS, Khumcha B, McCallum G, Miller JE, Morello R, Munro APS, Openshaw PJM, Padmanabhan S, Phongsamart W, Reubenson G, Ritz N, Rodrigues F, Rungmaitree S, Russell F, Sáfadi MAP, Saner C, Semple MG, Prado da Silva DGB, de Sousa LMM, Diogo Moço Souza M, Spann K, Walaza S, Wolter N, Xia Y, Yeoh DK, Zar HJ, Zimmermann P, Short KR. International Pediatric COVID-19 Severity Over the Course of the Pandemic. JAMA Pediatr 2023; 177:1073-1084. [PMID: 37603343 PMCID: PMC10442787 DOI: 10.1001/jamapediatrics.2023.3117] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/21/2023] [Indexed: 08/22/2023]
Abstract
Importance Multiple SARS-CoV-2 variants have emerged over the COVID-19 pandemic. The implications for COVID-19 severity in children worldwide are unclear. Objective To determine whether the dominant circulating SARS-CoV-2 variants of concern (VOCs) were associated with differences in COVID-19 severity among hospitalized children. Design, Setting, and Participants Clinical data from hospitalized children and adolescents (younger than 18 years) who were SARS-CoV-2 positive were obtained from 9 countries (Australia, Brazil, Italy, Portugal, South Africa, Switzerland, Thailand, UK, and the US) during 3 different time frames. Time frames 1 (T1), 2 (T2), and 3 (T3) were defined to represent periods of dominance by the ancestral virus, pre-Omicron VOCs, and Omicron, respectively. Age groups for analysis were younger than 6 months, 6 months to younger than 5 years, and 5 to younger than 18 years. Children with an incidental positive test result for SARS-CoV-2 were excluded. Exposures SARS-CoV-2 hospitalization during the stipulated time frame. Main Outcomes and Measures The severity of disease was assessed by admission to intensive care unit (ICU), the need for ventilatory support, or oxygen therapy. Results Among 31 785 hospitalized children and adolescents, the median age was 4 (IQR 1-12) years and 16 639 were male (52.3%). In children younger than 5 years, across successive SARS-CoV-2 waves, there was a reduction in ICU admission (T3 vs T1: risk ratio [RR], 0.56; 95% CI, 0.42-0.75 [younger than 6 months]; RR, 0.61, 95% CI; 0.47-0.79 [6 months to younger than 5 years]), but not ventilatory support or oxygen therapy. In contrast, ICU admission (T3 vs T1: RR, 0.39, 95% CI, 0.32-0.48), ventilatory support (T3 vs T1: RR, 0.37; 95% CI, 0.27-0.51), and oxygen therapy (T3 vs T1: RR, 0.47; 95% CI, 0.32-0.70) decreased across SARS-CoV-2 waves in children 5 years to younger than 18 years old. The results were consistent when data were restricted to unvaccinated children. Conclusions and Relevance This study provides valuable insights into the impact of SARS-CoV-2 VOCs on the severity of COVID-19 in hospitalized children across different age groups and countries, suggesting that while ICU admissions decreased across the pandemic in all age groups, ventilatory and oxygen support generally did not decrease over time in children aged younger than 5 years. These findings highlight the importance of considering different pediatric age groups when assessing disease severity in COVID-19.
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Affiliation(s)
- Yanshan Zhu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Flávia Jacqueline Almeida
- Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
- Hospital Infantil Sabará, Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
| | - J Kenneth Baillie
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Asha C Bowen
- Department of Infectious Diseases, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Philip N Britton
- Department of Infectious Diseases and Microbiology, the Children's Hospital, Westmead, New South Wales, Australia
- Sydney Medical School and Sydney Infectious Diseases, University of Sydney, Sydney, New South Wales, Australia
| | | | - Danilo Buonsenso
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - David Burgner
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Department of General Medicine, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - Keng Yih Chew
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Kulkanya Chokephaibulkit
- Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, 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
| | - Stephania A Cormier
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana
- Pennington Biomedical Research Center, Baton Rouge, Louisiana
| | - Nigel Crawford
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of General Medicine, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - Nigel Curtis
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Infectious Diseases, The Royal Children's Hospital Melbourne, Parkville, Victoria, Australia
| | - Camila G A Farias
- Hospital Infantil Sabará, Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
| | - Charles F Gilks
- School of Public Health, The University of Queensland, Brisbane, Queensland, Australia
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Diana Hamer
- Our Lady of the Lake Children's Hospital, Baton Rouge, Louisiana
| | - Daniel Jarovsky
- Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
- Hospital Infantil Sabará, Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
| | - Waasila Jassat
- Division of the National Health Laboratory Services, National Institute of Communicable Diseases, Johannesburg, South Africa
| | - Ana Rita Jesus
- Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Lisa S Kemp
- Our Lady of the Lake Children's Hospital, Baton Rouge, Louisiana
| | - Benjawan Khumcha
- Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Georgina McCallum
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Jessica E Miller
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Rosa Morello
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Alasdair P S Munro
- NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Imperial College Healthcare NHS Trust: London, London, United Kingdom
| | - Srivatsan Padmanabhan
- Elson S. Floyd College of Medicine, Washington State University, Tacoma, Washington
- St Joseph Medical Center, Tacoma, Washington
| | - Wanatpreeya Phongsamart
- Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Gary Reubenson
- Empilweni Service & Research Unit, Rahima Moosa Mother & Child Hospital, Department of Paediatrics & Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Ritz
- Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Mycobacterial and Migrant Health Research Group, University of Basel Children's Hospital Basel and Department of Clinical Research, University of Basel, Basel, Switzerland
- Department of Pediatrics and Pediatric Infectious Diseases, Children's Hospital Lucerne and Faculty of Health Science and Medicine, University of Lucerne, Lucerne, Switzerland
| | - Fernanda Rodrigues
- Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Supattra Rungmaitree
- Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Fiona Russell
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Marco A P Sáfadi
- Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
- Hospital Infantil Sabará, Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
| | - Christoph Saner
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
- Division of Pediatric Endocrinology, Diabetology and Metabolism, Department of Pediatrics, University Hospital Inselspital, University of Bern, Bern, Switzerland
- Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Malcolm G Semple
- NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Alder Hey Children's Hospital, Liverpool, United Kingdom
| | | | | | | | - Kirsten Spann
- Centre for Immunology and Infection Control, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, 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
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Yao Xia
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Daniel K Yeoh
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, SA- MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Petra Zimmermann
- Department of Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Kirsty R Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
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7
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Jassat W, Reyes LF, Munblit D, Caoili J, Bozza F, Hashmi M, Edelstein M, Cohen C, Alvarez-Moreno CA, Cao B. Long COVID in low-income and middle-income countries: the hidden public health crisis. Lancet 2023; 402:1115-1117. [PMID: 37652071 DOI: 10.1016/s0140-6736(23)01685-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/09/2023] [Indexed: 09/02/2023]
Affiliation(s)
- Waasila Jassat
- National Institute for Communicable Diseases, Sandringham, Johannesburg 2192, South Africa; Genesis Analytics, Johannesburg, South Africa.
| | | | - Daniel Munblit
- Division of Care in Long Term Conditions, King's College London, London, UK; Department of Paediatrics and Paediatric Infectious Diseases, Sechenov University, Moscow, Russia
| | | | | | - Madiha Hashmi
- Department of Critical Care Medicine, Ziauddin University, Karachi, Pakistan
| | | | - Cheryl Cohen
- National Institute for Communicable Diseases, Sandringham, Johannesburg 2192, South Africa
| | | | - Bin Cao
- National Center for Respiratory Medicine, Beijing, China; Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
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8
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Hojo-Souza NS, Jassat W, Guidoni DL, de Souza FSH. Risks of Adverse Outcomes for Hospitalized COVID-19 Patients during the Four Waves in Brazil According to SARS-CoV-2 Variants, Age Group, and Vaccine Status. Viruses 2023; 15:1997. [PMID: 37896773 PMCID: PMC10610718 DOI: 10.3390/v15101997] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 10/29/2023] Open
Abstract
Brazil was hit with four consecutive waves of COVID-19 until 2022 due to the ancestral SARS-CoV-2 (B.1 lineage), followed by the emergence of variants/subvariants. Relative risks of adverse outcomes for COVID-19 patients hospitalized during the four waves were evaluated. Data were extracted from the largest Brazilian database (SIVEP-Gripe), and COVID-19 patients who were hospitalized during the peak of each of the four waves (15-week intervals) were included in this study. The outcomes of in-hospital death, invasive (IMV) and non-invasive (NIV) ventilation requirements, and intensive care unit (ICU) admission were analyzed to estimate the relative risks. A higher risk of in-hospital death was found during the second wave for all age groups, but a significant reduction was observed in the risk of death for the elderly during the third and fourth waves compared to patients in the first wave. There was an increased risk of IMV requirement and ICU admissions during the second wave for patients aged 18-59 years old compared to the first wave. Relative risk analysis showed that booster-vaccinated individuals have lower risks of in-hospital death and IMV requirement in all age groups compared to unvaccinated/partially vaccinated patients, demonstrating the relevance of full/booster vaccination in reducing adverse outcomes for patients who were hospitalized during the variant prevalence.
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Affiliation(s)
- Natália Satchiko Hojo-Souza
- Laboratory of Immunopathology, Oswaldo Cruz Foundation—Minas, Av. Augusto de Lima, 1715, Belo Horizonte 30190-002, MG, Brazil
| | - Waasila Jassat
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - Daniel Ludovico Guidoni
- Department of Computing, Federal University of Ouro Preto, Morro do Cruzeiro Campus, Ouro Preto 35400-000, MG, Brazil
| | - Fernanda Sumika Hojo de Souza
- Department of Computing, Federal University of Ouro Preto, Morro do Cruzeiro Campus, Ouro Preto 35400-000, MG, Brazil
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9
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Bingham J, Tempia S, Moultrie H, Viboud C, Jassat W, Cohen C, Pulliam JR. Estimating the time-varying reproduction number for COVID-19 in South Africa during the first four waves using multiple measures of incidence for public and private sectors across four waves. PLoS One 2023; 18:e0287026. [PMID: 37738280 PMCID: PMC10516415 DOI: 10.1371/journal.pone.0287026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/30/2023] [Indexed: 09/24/2023] Open
Abstract
OBJECTIVES The aim of this study was to quantify transmission trends in South Africa during the first four waves of the COVID-19 pandemic using estimates of the time-varying reproduction number (R) and to compare the robustness of R estimates based on three different data sources, and using data from public and private sector service providers. METHODS R was estimated from March 2020 through April 2022, nationally and by province, based on time series of rt-PCR-confirmed cases, hospitalisations, and hospital-associated deaths, using a method that models daily incidence as a weighted sum of past incidence, as implemented in the R package EpiEstim. R was also estimated separately using public and private sector data. RESULTS Nationally, the maximum case-based R following the introduction of lockdown measures was 1.55 (CI: 1.43-1.66), 1.56 (CI: 1.47-1.64), 1.46 (CI: 1.38-1.53) and 3.33 (CI: 2.84-3.97) during the first (Wuhan-Hu), second (Beta), third (Delta), and fourth (Omicron) waves, respectively. Estimates based on the three data sources (cases, hospitalisations, deaths) were generally similar during the first three waves, but higher during the fourth wave for case-based estimates. Public and private sector R estimates were generally similar except during the initial lockdowns and in case-based estimates during the fourth wave. CONCLUSION Agreement between R estimates using different data sources during the first three waves suggests that data from any of these sources could be used in the early stages of a future pandemic. The high R estimates for Omicron relative to earlier waves are interesting given a high level of exposure pre-Omicron. The agreement between public and private sector R estimates highlights that clients of the public and private sectors did not experience two separate epidemics, except perhaps to a limited extent during the strictest lockdowns in the first wave.
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Affiliation(s)
- Jeremy Bingham
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Harry Moultrie
- Division of the National Health Laboratory Service, Centre for Tuberculosis, National Institute for Communicable Diseases, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cecile Viboud
- Fogarty International Center, NIH, Bethesda, MD, United States of America
| | - Waasila Jassat
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- Right to Care, Pretoria, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Juliet R.C. Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
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10
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Vadlamudi NK, Basham CA, Johnston JC, Ahmad Khan F, Battista Migliori G, Centis R, D'Ambrosio L, Jassat W, Davies MA, Schwartzman K, Campbell JR. The association of SARS-CoV-2 infection and tuberculosis disease with unfavorable treatment outcomes: A systematic review. PLOS Glob Public Health 2023; 3:e0002163. [PMID: 37467225 DOI: 10.1371/journal.pgph.0002163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 05/28/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Whether SARS-CoV-2 infection and its management influence tuberculosis (TB) treatment outcomes is uncertain. We synthesized evidence on the association of SARS-CoV-2 coinfection (Coinfection Review) and its management (Clinical Management Review) on treatment outcomes among people with tuberculosis (TB) disease. METHODS We systematically searched the literature from 1 January 2020 to 6 February 2022. Primary outcomes included: unfavorable (death, treatment failure, loss-to-follow-up) TB treatment outcomes (Coinfection and Clinical Management Review) and/or severe or critical COVID-19 or death (Clinical Management Review). Study quality was assessed with an adapted Newcastle Ottawa Scale. Data were heterogeneous and a narrative review was performed. An updated search was performed on April 3, 2023. FINDINGS From 9,529 records, we included 11 studies and 7305 unique participants. No study reported data relevant to our review in their primary publication and data had to be contributed by study authors after contact. Evidence from all studies was low quality. Eight studies of 5749 persons treated for TB (286 [5%] with SARS-CoV-2) were included in the Coinfection Review. Across five studies reporting our primary outcome, there was no significant association between SARS-CoV-2 coinfection and unfavorable TB treatment outcomes. Four studies of 1572 TB patients-of whom 291 (19%) received corticosteroids or other immunomodulating treatment-were included in the Clinical Management Review, and two addressed a primary outcome. Studies were likely confounded by indication and discordant findings existed among studies. When updating our search, we still did not identify any study reporting data relevant to this review in their primary publication. INTERPRETATION No study was designed to answer our research questions of interest. It remains unclear whether TB/SARS-CoV-2 and its therapeutic management are associated with unfavorable outcomes. Research is needed to improve our understanding of risk and optimal management of persons with TB and SARS-CoV-2 infection. TRIAL REGISTRATION Registration: PROSPERO (CRD42022309818).
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Affiliation(s)
- Nirma Khatri Vadlamudi
- Faculty of Medicine, Department of Pediatrics, The University of British Columbia, Vancouver, Canada
| | - C Andrew Basham
- Division of Pharmacoepidemiology and Pharmacoeconomics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - James C Johnston
- Faculty of Medicine, Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Faiz Ahmad Khan
- Research Institute of the McGill University Health Centre, Respiratory Epidemiology and Clinical Research Unit, Centre for Outcomes Research & Evaluation, Montreal, Canada
- McGill International TB Centre, Montreal, Canada
| | - Giovanni Battista Migliori
- Istituti Clinici Scientifici Maugeri IRCCS, Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Tradate, Italy
| | - Rosella Centis
- Istituti Clinici Scientifici Maugeri IRCCS, Servizio di Epidemiologia Clinica delle Malattie Respiratorie, Tradate, Italy
| | | | - Waasila Jassat
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service, Division of Public Health Surveillance and Response, Johannesburg, South Africa
- Right to Care, Pretoria, South Africa
| | - Mary-Ann Davies
- Western Cape Government, Health and Wellness, Cape Town, South Africa
- School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Kevin Schwartzman
- Research Institute of the McGill University Health Centre, Respiratory Epidemiology and Clinical Research Unit, Centre for Outcomes Research & Evaluation, Montreal, Canada
- McGill International TB Centre, Montreal, Canada
- Respiratory Division, McGill University, Montreal, Canada
| | - Jonathon R Campbell
- Research Institute of the McGill University Health Centre, Respiratory Epidemiology and Clinical Research Unit, Centre for Outcomes Research & Evaluation, Montreal, Canada
- McGill International TB Centre, Montreal, Canada
- Department of Medicine & Department of Global and Public Health, McGill University, Montreal, Canada
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11
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Maposa I, Welch R, Ozougwu L, Arendse T, Mudara C, Blumberg L, Jassat W. Using generalized structured additive regression models to determine factors associated with and clusters for COVID-19 hospital deaths in South Africa. BMC Public Health 2023; 23:830. [PMID: 37147648 PMCID: PMC10161152 DOI: 10.1186/s12889-023-15789-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 04/30/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND The first case of COVID-19 in South Africa was reported in March 2020 and the country has since recorded over 3.6 million laboratory-confirmed cases and 100 000 deaths as of March 2022. Transmission and infection of SARS-CoV-2 virus and deaths in general due to COVID-19 have been shown to be spatially associated but spatial patterns in in-hospital deaths have not fully been investigated in South Africa. This study uses national COVID-19 hospitalization data to investigate the spatial effects on hospital deaths after adjusting for known mortality risk factors. METHODS COVID-19 hospitalization data and deaths were obtained from the National Institute for Communicable Diseases (NICD). Generalized structured additive logistic regression model was used to assess spatial effects on COVID-19 in-hospital deaths adjusting for demographic and clinical covariates. Continuous covariates were modelled by assuming second-order random walk priors, while spatial autocorrelation was specified with Markov random field prior and fixed effects with vague priors respectively. The inference was fully Bayesian. RESULTS The risk of COVID-19 in-hospital mortality increased with patient age, with admission to intensive care unit (ICU) (aOR = 4.16; 95% Credible Interval: 4.05-4.27), being on oxygen (aOR = 1.49; 95% Credible Interval: 1.46-1.51) and on invasive mechanical ventilation (aOR = 3.74; 95% Credible Interval: 3.61-3.87). Being admitted in a public hospital (aOR = 3.16; 95% Credible Interval: 3.10-3.21) was also significantly associated with mortality. Risk of in-hospital deaths increased in months following a surge in infections and dropped after months of successive low infections highlighting crest and troughs lagging the epidemic curve. After controlling for these factors, districts such as Vhembe, Capricorn and Mopani in Limpopo province, and Buffalo City, O.R. Tambo, Joe Gqabi and Chris Hani in Eastern Cape province remained with significantly higher odds of COVID-19 hospital deaths suggesting possible health systems challenges in those districts. CONCLUSION The results show substantial COVID-19 in-hospital mortality variation across the 52 districts. Our analysis provides information that can be important for strengthening health policies and the public health system for the benefit of the whole South African population. Understanding differences in in-hospital COVID-19 mortality across space could guide interventions to achieve better health outcomes in affected districts.
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Affiliation(s)
- Innocent Maposa
- Division of Epidemiology & Biostatistics, School of Public Health, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa.
- Division of Epidemiology & Biostatistics, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, Cape Town, South Africa.
| | - Richard Welch
- National Institute for Communicable Diseases, Johannesburg, South Africa
- Right to Care, Centurion, Johannesburg, South Africa
| | - Lovelyn Ozougwu
- National Institute for Communicable Diseases, Johannesburg, South Africa
- Right to Care, Centurion, Johannesburg, South Africa
| | - Tracy Arendse
- National Institute for Communicable Diseases, Johannesburg, South Africa
- Right to Care, Centurion, Johannesburg, South Africa
| | - Caroline Mudara
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Lucille Blumberg
- National Institute for Communicable Diseases, Johannesburg, South Africa
- Right to Care, Centurion, Johannesburg, South Africa
| | - Waasila Jassat
- National Institute for Communicable Diseases, Johannesburg, South Africa
- Right to Care, Centurion, Johannesburg, South Africa
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12
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Reid J, Daya R, Zingoni ZM, Jassat W, Bayat Z, Nel J. COVID-19 in-hospital mortality during the first two pandemic waves, at Helen Joseph Hospital, South Africa. Pan Afr Med J 2023; 45:5. [PMID: 37346915 PMCID: PMC10280698 DOI: 10.11604/pamj.2023.45.5.39222] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/19/2023] [Indexed: 06/23/2023] Open
Abstract
Introduction there has been significant global variation in Coronavirus Disease (COVID-19) mortality at different time points in the pandemic. Contributing factors include population demographics, comorbidities, health system capacity, prior infection with COVID-19, vaccinations, and viral variants. The study aims to describe COVID-19-related mortality of inpatients at Helen Joseph Hospital (HJH), over 12 months, during the first two waves of the COVID-19 pandemic in South Africa. The primary objectives were to describe the socio-demographic details, clinical characteristics, and hospital outcomes during the first and second waves of COVID-19. This included an assessment of the in-hospital case fatality ratio (CFR) of patients admitted with COVID-19. The secondary objectives were to compare the socio-demographic details, clinical characteristics, and outcomes between the two waves, and to determine risk factors associated with COVID-19-related mortality. Methods this is a retrospective cohort study of all inpatient laboratory-confirmed COVID-19 cases at HJH from 1st May 2020 to 31st April 2021. Data were collected by the National Institute for Communicable Diseases (NICD). Bivariate analysis was performed to describe and compare the socio-demographic characteristics, clinical characteristics, and hospital admission outcomes between the two waves. Multivariate logistic regression was used to determine risk factors for COVID-19-related mortality. Results overall, 1359 patients were admitted, 595 in wave one, and 764 in wave two. Patients were predominantly male (52.4%), of Black African race (75.1%) with a mean age of 54.6 (standard deviation 15.4) years. The median length of stay was 8 days (interquartile range 5-14 days). In total, 73.2% (995) of patients required oxygen, 5.2% (71) of patients received mechanical ventilation, and 7.1% (96) were admitted to the high care and Intensive Care Unit (ICU). The most common comorbid illnesses were hypertension (36.7%, n=499), diabetes mellitus (26.6%, n=362), Human Immunodeficiency Virus (HIV) (10.8%, n=147), and obesity (11.0%, n=149). The in-hospital CFR during the first wave was 30.4% (181/595) and 25.5% (195/764) (p<0.001) in the second wave, and overall, in-hospital CFR was 27.7% (376/1359). The adjusted odds of death were 79% higher among patients admitted during wave one compared to wave two (aOR=1.79; 95% CI: 1.35-2.38). A one-year increase in age increased the odds of death by 4% (aOR=1.04; 95% CI: 1.03-1.05). The need for oxygen (aOR=2.17, 95%CI: 1.56-3.01) and ventilation (aOR=7.23, 95% CI: 4.02-13.01) were significant risk factors for mortality. Conclusion prior to the availability of vaccines, COVID-19-related mortality was high and risk factors for mortality were consistent with national and international findings. This study reflects the impact of the pandemic on the South African public sector with limited resources and minimal ICU capacity.
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Affiliation(s)
- Joanna Reid
- Department of Internal Medicine, Helen Joseph Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Reyna Daya
- Department of Internal Medicine, Helen Joseph Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zvifadzo Matsena Zingoni
- Division of Epidemiology and Biostatistics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Waasila Jassat
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), South Africa
- Right to Care, Centurion, South Africa
| | - Zaheer Bayat
- Department of Internal Medicine, Helen Joseph Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jeremy Nel
- Department of Internal Medicine, Helen Joseph Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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13
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Kartsonaki C, Baillie JK, Barrio NG, Baruch J, Beane A, Blumberg L, Bozza F, Broadley T, Burrell A, Carson G, Citarella BW, Dagens A, Dankwa EA, Donnelly CA, Dunning J, Elotmani L, Escher M, Farshait N, Goffard JC, Gonçalves BP, Hall M, Hashmi M, Sim Lim Heng B, Ho A, Jassat W, Pedrera Jiménez M, Laouenan C, Lissauer S, Martin-Loeches I, Mentré F, Merson L, Morton B, Munblit D, Nekliudov NA, Nichol AD, Singh Oinam BC, Ong D, Panda PK, Petrovic M, Pritchard MG, Ramakrishnan N, Ramos GV, Roger C, Sandulescu O, Semple MG, Sharma P, Sigfrid L, Somers EC, Streinu-Cercel A, Taccone F, Vecham PK, Kumar Tirupakuzhi Vijayaraghavan B, Wei J, Wils EJ, Ci Wong X, Horby P, Rojek A, Olliaro PL. Characteristics and outcomes of an international cohort of 600 000 hospitalized patients with COVID-19. Int J Epidemiol 2023; 52:355-376. [PMID: 36850054 PMCID: PMC10114094 DOI: 10.1093/ije/dyad012] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 02/01/2023] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND We describe demographic features, treatments and clinical outcomes in the International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) COVID-19 cohort, one of the world's largest international, standardized data sets concerning hospitalized patients. METHODS The data set analysed includes COVID-19 patients hospitalized between January 2020 and January 2022 in 52 countries. We investigated how symptoms on admission, co-morbidities, risk factors and treatments varied by age, sex and other characteristics. We used Cox regression models to investigate associations between demographics, symptoms, co-morbidities and other factors with risk of death, admission to an intensive care unit (ICU) and invasive mechanical ventilation (IMV). RESULTS Data were available for 689 572 patients with laboratory-confirmed (91.1%) or clinically diagnosed (8.9%) SARS-CoV-2 infection from 52 countries. Age [adjusted hazard ratio per 10 years 1.49 (95% CI 1.48, 1.49)] and male sex [1.23 (1.21, 1.24)] were associated with a higher risk of death. Rates of admission to an ICU and use of IMV increased with age up to age 60 years then dropped. Symptoms, co-morbidities and treatments varied by age and had varied associations with clinical outcomes. The case-fatality ratio varied by country partly due to differences in the clinical characteristics of recruited patients and was on average 21.5%. CONCLUSIONS Age was the strongest determinant of risk of death, with a ∼30-fold difference between the oldest and youngest groups; each of the co-morbidities included was associated with up to an almost 2-fold increase in risk. Smoking and obesity were also associated with a higher risk of death. The size of our international database and the standardized data collection method make this study a comprehensive international description of COVID-19 clinical features. Our findings may inform strategies that involve prioritization of patients hospitalized with COVID-19 who have a higher risk of death.
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Affiliation(s)
- Christiana Kartsonaki
- Medical Research Council (MRC) Population Health Research Unit, Clinical Trials Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | | | - Joaquín Baruch
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Lucille Blumberg
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Fernando Bozza
- National Institute of Infectious Disease Evandro Chagas, Oswaldo Cruz Foundation (INI-FIOCRUZ), Ministry of Health, and D'Or Institute of Research and Education (IDOR), Rio de Janeiro, São Paulo, Brazil
| | | | | | - Gail Carson
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Barbara Wanjiru Citarella
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew Dagens
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Christl A Donnelly
- Department of Statistics, University of Oxford, Oxford, UK
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Jake Dunning
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Martina Escher
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | - Bronner P Gonçalves
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Madiha Hashmi
- Critical Care Asia and Ziauddin University, Karachi, Pakistan
| | | | - Antonia Ho
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK Department of Infectious Diseases, Queen Elizabeth University Hospital, Glasgow, UK
| | - Waasila Jassat
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | | | - Cedric Laouenan
- Université de Paris, France, Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, Paris, France
| | | | | | - France Mentré
- Université de Paris, France, Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, Paris, France
| | - Laura Merson
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Infectious Diseases Data Observatory, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Ben Morton
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Daniel Munblit
- Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child’s Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
- Inflammation, Repair and Development Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | | | - Alistair D Nichol
- Irish Critical Care Critical Clinical Trials Network, Dublin, Ireland
| | | | - David Ong
- Franciscus Gasthuis & Vlietland, Rotterdam, Netherlands
| | | | | | - Mark G Pritchard
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Grazielle Viana Ramos
- National Institute of Infectious Disease Evandro Chagas, Oswaldo Cruz Foundation (INI-FIOCRUZ), Ministry of Health, and D'Or Institute of Research and Education (IDOR), Rio de Janeiro, São Paulo, Brazil
| | | | - Oana Sandulescu
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
- National Institute for Infectious Diseases ‘Prof. Dr. Matei Bals’, Bucharest, Romania
| | - Malcolm G Semple
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- UK Respiratory Medicine, Alder Hey Children’s NHS Foundation Trust, Liverpool, UK
| | - Pratima Sharma
- University of Michigan Schools of Medicine & Public Health, Ann Arbor, Michigan, USA
| | - Louise Sigfrid
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Emily C Somers
- University of Michigan Schools of Medicine & Public Health, Ann Arbor, Michigan, USA
| | | | - Fabio Taccone
- Cliniques Universitaires de Bruxelles (CUB) Hopital Erasme, Anderlecht, Belgium
| | | | | | - Jia Wei
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Xin Ci Wong
- National Institutes of Health (NIH), Ministry of Health, Shah Alam, Malaysia
| | - Peter Horby
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Amanda Rojek
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Royal Melbourne Hospital, Melbourne, Australia
- Centre for Integrated Critical Care, University of Melbourne, Melbourne, Australia
| | - Piero L Olliaro
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Global Support Centre, Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Jassat W, Abdool Karim SS, Ozougwu L, Welch R, Mudara C, Masha M, Rousseau P, Wolmarans M, Selikow A, Govender N, Walaza S, von Gottberg A, Wolter N, Terrence Pisa P, Sanne I, Govender S, Blumberg L, Cohen C, Groome MJ. Trends in Cases, Hospitalizations, and Mortality Related to the Omicron BA.4/BA.5 Subvariants in South Africa. Clin Infect Dis 2023; 76:1468-1475. [PMID: 36453094 PMCID: PMC10110264 DOI: 10.1093/cid/ciac921] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/16/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND In this study, we compared admission incidence risk and the risk of mortality in the Omicron BA.4/BA.5 wave to previous waves. METHODS Data from South Africa's SARS-CoV-2 case linelist, national COVID-19 hospital surveillance system, and Electronic Vaccine Data System were linked and analyzed. Wave periods were defined when the country passed a weekly incidence of 30 cases/100 000 population. In-hospital case fatality ratios (CFRs) during the Delta, Omicron BA.1/BA.2, and Omicron BA.4/BA.5 waves were compared using post-imputation random effect multivariable logistic regression models. RESULTS The CFR was 25.9% (N = 37 538 of 144 778), 10.9% (N = 6123 of 56 384), and 8.2% (N = 1212 of 14 879) in the Delta, Omicron BA.1/BA.2, and Omicron BA.4/BA.5 waves, respectively. After adjusting for age, sex, race, comorbidities, health sector, and province, compared with the Omicron BA.4/BA.5 wave, patients had higher risk of mortality in the Omicron BA.1/BA.2 wave (adjusted odds ratio [aOR], 1.3; 95% confidence interval [CI]: 1.2-1.4) and Delta wave (aOR, 3.0; 95% CI: 2.8-3.2). Being partially vaccinated (aOR, 0.9; 95% CI: .9-.9), fully vaccinated (aOR, 0.6; 95% CI: .6-.7), and boosted (aOR, 0.4; 95% CI: .4-.5) and having prior laboratory-confirmed infection (aOR, 0.4; 95% CI: .3-.4) were associated with reduced risks of mortality. CONCLUSIONS Overall, admission incidence risk and in-hospital mortality, which had increased progressively in South Africa's first 3 waves, decreased in the fourth Omicron BA.1/BA.2 wave and declined even further in the fifth Omicron BA.4/BA.5 wave. Mortality risk was lower in those with natural infection and vaccination, declining further as the number of vaccine doses increased.
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Affiliation(s)
- Waasila Jassat
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- Right to Care, Pretoria, South Africa
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Lovelyn Ozougwu
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- Right to Care, Pretoria, South Africa
| | - Richard Welch
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- Right to Care, Pretoria, South Africa
| | - Caroline Mudara
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Maureen Masha
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- Right to Care, Pretoria, South Africa
| | | | | | - Anthony Selikow
- Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Nevashan Govender
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Sibongile Walaza
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Pedro Terrence Pisa
- Right to Care, Pretoria, South Africa
- Department of Human Nutrition and Dietetics, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Ian Sanne
- Right to Care, Pretoria, South Africa
- Clinical HIV Research Unit, Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Lucille Blumberg
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- Right to Care, Pretoria, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Michelle J Groome
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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15
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Jassat W, Mudara C, Vika C, Welch R, Arendse T, Dryden M, Blumberg L, Mayet N, Tempia S, Parker A, Nel J, Perumal R, Groome MJ, Conradie F, Ndjeka N, Sigfrid L, Merson L, Cohen C. A cohort study of post-COVID-19 condition across the Beta, Delta, and Omicron waves in South Africa: 6-month follow-up of hospitalized and nonhospitalized participants. Int J Infect Dis 2023; 128:102-111. [PMID: 36587841 PMCID: PMC9800016 DOI: 10.1016/j.ijid.2022.12.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES The study aimed to describe the prevalence of and risk factors for post-COVID-19 condition (PCC). METHODS This was a prospective, longitudinal observational cohort study. Hospitalized and nonhospitalized adults were randomly selected to undergo telephone assessment at 1, 3, and 6 months. Participants were assessed using a standardized questionnaire for the evaluation of symptoms and health-related quality of life. We used negative binomial regression models to determine factors associated with the presence of ≥1 symptoms at 6 months. RESULTS A total of 46.7% of hospitalized and 18.5% of nonhospitalized participants experienced ≥1 symptoms at 6 months (P ≤0.001). Among hospitalized people living with HIV, 40.4% had persistent symptoms compared with 47.1% among participants without HIV (P = 0.108). The risk factors for PCC included older age, female sex, non-Black race, presence of a comorbidity, greater number of acute COVID-19 symptoms, hospitalization/COVID-19 severity, and wave period (lower risk of persistent symptoms for the Omicron compared with the Beta wave). There were no associations between self-reported vaccination status with persistent symptoms. CONCLUSION The study revealed a high prevalence of persistent symptoms among South African participants at 6 months but decreased risk for PCC among participants infected during the Omicron BA.1 wave. These findings have serious implications for countries with resource-constrained health care systems.
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Affiliation(s)
- Waasila Jassat
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa; Right to Care, Centurion, South Africa.
| | - Caroline Mudara
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa
| | - Caroline Vika
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa
| | - Richard Welch
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa; Right to Care, Centurion, South Africa
| | - Tracy Arendse
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa; Right to Care, Centurion, South Africa
| | - Murray Dryden
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa
| | - Lucille Blumberg
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa; Right to Care, Centurion, South Africa
| | - Natalie Mayet
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa
| | - Stefano Tempia
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Arifa Parker
- Divisions of General Medicine and Infectious Diseases, Faculty of Medicine and Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Jeremy Nel
- Division of Infectious Diseases, Department of Medicine, University of the Witwatersrand, Johannesburg, South Africa
| | - Rubeshan Perumal
- Division of Pulmonology and Critical Care, Department of Medicine, University of KwaZulu-Natal, Berea, Durban, South Africa; South African Medical Research Council-CAPRISA HIV/TB Pathogenesis and Treatment Research Unit, Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Michelle J Groome
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Francesca Conradie
- Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Norbert Ndjeka
- Drug-Resistant TB, TB & HIV Directorate, National Department of Health, Pretoria, South Africa and University of KwaZulu-Natal, Durban, South Africa
| | - Louise Sigfrid
- International Severe Acute Respiratory and emerging Infections Consortium (ISARIC), Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
| | - Laura Merson
- International Severe Acute Respiratory and emerging Infections Consortium (ISARIC), Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
| | - Cheryl Cohen
- National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Madhi SA, Kwatra G, Myers JE, Jassat W, Dhar N, Mukendi CK, Blumberg L, Welch R, Izu A, Mutevedzi PC. Sustained Low Incidence of Severe and Fatal COVID-19 Following Widespread Infection Induced Immunity after the Omicron (BA.1) Dominant in Gauteng, South Africa: An Observational Study. Viruses 2023; 15:v15030597. [PMID: 36992306 PMCID: PMC10054630 DOI: 10.3390/v15030597] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/15/2023] [Accepted: 02/18/2023] [Indexed: 02/24/2023] Open
Abstract
We conducted an epidemiologic survey to determine the seroprevalence of SARS-CoV-2 anti-nucleocapsid (anti-N) and anti-spike (anti-S) protein IgG from 1 March to 11 April 2022 after the BA.1-dominant wave had subsided in South Africa and prior to another wave dominated by the BA.4 and BA.5 (BA.4/BA.5) sub-lineages. We also analysed epidemiologic trends in Gauteng Province for cases, hospitalizations, recorded deaths, and excess deaths were evaluated from the inception of the pandemic through 17 November 2022. Despite only 26.7% (1995/7470) of individuals having received a COVID-19 vaccine, the overall seropositivity for SARS-CoV-2 was 90.9% (95% confidence interval (CI), 90.2 to 91.5) at the end of the BA.1 wave, and 64% (95% CI, 61.8 to 65.9) of individuals were infected during the BA.1-dominant wave. The SARS-CoV-2 infection fatality risk was 16.5–22.3 times lower in the BA.1-dominant wave compared with the pre-BA.1 waves for recorded deaths (0.02% vs. 0.33%) and estimated excess mortality (0.03% vs. 0.67%). Although there are ongoing cases of COVID-19 infections, hospitalization and death, there has not been any meaningful resurgence of COVID-19 since the BA.1- dominant wave despite only 37.8% coverage by at least a single dose of COVID-19 vaccine in Gauteng, South Africa.
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Affiliation(s)
- Shabir A. Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
- Infectious Diseases and Oncology Research Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
- Correspondence: ; Tel.: +27-82-8706672
| | - Gaurav Kwatra
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
- Infectious Diseases and Oncology Research Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Jonathan E. Myers
- Centre for Environmental and Occupational Health Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town 7701, South Africa
| | - Waasila Jassat
- National Health Laboratory Services, National Institute for Communicable Diseases, Johannesburg 2193, South Africa
- Right to Care, Centurion 0046, South Africa
| | - Nisha Dhar
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Christian K. Mukendi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Lucille Blumberg
- National Health Laboratory Services, National Institute for Communicable Diseases, Johannesburg 2193, South Africa
- Right to Care, Centurion 0046, South Africa
| | - Richard Welch
- National Health Laboratory Services, National Institute for Communicable Diseases, Johannesburg 2193, South Africa
- Right to Care, Centurion 0046, South Africa
| | - Alane Izu
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
- Infectious Diseases and Oncology Research Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Portia C. Mutevedzi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
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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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18
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Chiwandire N, Jassat W, Groome M, Kufa T, Walaza S, Wolter N, von Gottberg A, Zar HJ, Reubenson G, Tempia S, Ebonwu J, Govender N, Ntshoe G, Shonhiwa AM, Blumberg L, Cohen C. Changing epidemiology of COVID-19 in children and adolescents over four successive epidemic waves in South Africa, 2020-2022. J Pediatric Infect Dis Soc 2023; 12:128-134. [PMID: 36648247 PMCID: PMC10112681 DOI: 10.1093/jpids/piad002] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/16/2023] [Indexed: 01/18/2023]
Abstract
BACKGROUND South Africa experienced four waves of SARS-CoV-2 infection, dominated by Wuhan-Hu, Beta, Delta and Omicron (BA.1/BA.2). We describe the trends in SARS-CoV-2 testing, cases, admissions, and deaths among children and adolescents in South Africa over successive waves. METHODS We analysed national SARS-CoV-2 testing, case, and admissions data from March 2020 to February 2022 and estimated cumulative rates by age group for each endpoint. Severity in the third versus the fourth wave was assessed using multivariable logistic regression. RESULTS Individuals ≤18 years comprised 35% (21,008,060/60,142,978) of the population but only 12% (424,394/3,593,644) of cases and 6% (26,176/451,753) of admissions. Among individuals ≤18 years, infants had the highest admission (505/100,000) rates. Testing, case and admission rates generally increased successively in the second (Beta) and third (Delta) waves among all age groups. In the fourth (Omicron BA.1/BA.2) wave the case rate dropped among individuals ≥1-year but increased among those <1-year. Weekly admission rates for children <1-year (169/100,000) exceeded rates in adults (124/100,000) in the fourth wave. The odds of severe COVID-19 in all admitted cases were lower in the fourth wave versus the third wave in each age group, but they were twice as high in admitted cases with at least one comorbidity than those without. CONCLUSIONS The admission rate for children <5 years was higher in the fourth wave than previous waves, but the overall outcomes were less severe. However, children with at least one comorbidity had increased odds of severe disease, warranting consideration of prioritising this group for vaccination.
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Affiliation(s)
- Nicola Chiwandire
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Waasila Jassat
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,Right to Care, Johannesburg, South Africa
| | - Michelle Groome
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Tendesayi Kufa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Sibongile Walaza
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Public Health, University of the Witwatersrand, Johannesburg, 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
| | - Anne von Gottberg
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa.,MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Gary Reubenson
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Rahima Moosa Mother and Child Hospital, Johannesburg, South Africa
| | - Stefano Tempia
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Joy Ebonwu
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nevashan Govender
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Genevie Ntshoe
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Andronica Moipone Shonhiwa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Lucille Blumberg
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,Right to Care, Johannesburg, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
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19
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Jamieson L, Van Schalkwyk C, Nichols BE, Meyer-Rath G, Silal S, Pulliam J, Blumberg L, Cohen C, Moultrie H, Jassat W. Differential in-hospital mortality and intensive care treatment over time: Informing hospital pathways for modelling COVID-19 in South Africa. PLOS Glob Public Health 2023; 3:e0001073. [PMID: 37195977 DOI: 10.1371/journal.pgph.0001073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/15/2023] [Indexed: 05/19/2023]
Abstract
There are limited published data within sub-Saharan Africa describing hospital pathways of COVID-19 patients hospitalized. These data are crucial for the parameterisation of epidemiological and cost models, and for planning purposes for the region. We evaluated COVID-19 hospital admissions from the South African national hospital surveillance system (DATCOV) during the first three COVID-19 waves between May 2020 and August 2021. We describe probabilities and admission into intensive care units (ICU), mechanical ventilation, death, and lengths of stay (LOS) in non-ICU and ICU care in public and private sectors. A log-binomial model was used to quantify mortality risk, ICU treatment and mechanical ventilation between time periods, adjusting for age, sex, comorbidity, health sector and province. There were 342,700 COVID-19-related hospital admissions during the study period. Risk of ICU admission was 16% lower during wave periods (adjusted risk ratio (aRR) 0.84 [0.82-0.86]) compared to between-wave periods. Mechanical ventilation was more likely during a wave overall (aRR 1.18 [1.13-1.23]), but patterns between waves were inconsistent, while mortality risk in non-ICU and ICU were 39% (aRR 1.39 [1.35-1.43]) and 31% (aRR 1.31 [1.27-1.36]) higher during a wave, compared to between-wave periods, respectively. If patients had had the same probability of death during waves vs between-wave periods, we estimated approximately 24% [19%-30%] of deaths (19,600 [15,200-24,000]) would not have occurred over the study period. LOS differed by age (older patients stayed longer), ward type (ICU stays were longer than non-ICU) and death/recovery outcome (time to death was shorter in non-ICU); however, LOS remained similar between time periods. Healthcare capacity constraints as inferred by wave period have a large impact on in-hospital mortality. It is crucial for modelling health systems strain and budgets to consider how input parameters related to hospitalisation change during and between waves, especially in settings with severely constrained resources.
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Affiliation(s)
- Lise Jamieson
- Health Economics and Epidemiology Research Office (HE2RO), Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Medical Microbiology, Amsterdam University Medical Center, Amsterdam, The Netherlands
- The South African Department of Science and Innovation/National Research Foundation Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, Republic of South Africa
| | - Cari Van Schalkwyk
- The South African Department of Science and Innovation/National Research Foundation Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, Republic of South Africa
| | - Brooke E Nichols
- Health Economics and Epidemiology Research Office (HE2RO), Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Medical Microbiology, Amsterdam University Medical Center, Amsterdam, The Netherlands
- Department of Global Health, School of Public Health, Boston University, Boston, Massachusetts, United States of America
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - Gesine Meyer-Rath
- Health Economics and Epidemiology Research Office (HE2RO), Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- The South African Department of Science and Innovation/National Research Foundation Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, Republic of South Africa
- Department of Global Health, School of Public Health, Boston University, Boston, Massachusetts, United States of America
| | - Sheetal Silal
- Modelling and Simulation Hub, Africa, Department of Statistical Sciences, University of Cape Town, Cape Town, South Africa
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Juliet Pulliam
- The South African Department of Science and Innovation/National Research Foundation Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, Republic of South Africa
| | - Lucille Blumberg
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- Right to Care, Centurion, 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
| | - Harry Moultrie
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Waasila Jassat
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- Right to Care, Centurion, South Africa
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20
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Le Roux SR, Jassat W, Dickson L, Mitrani L, Cox H, Mlisana K, Black J, Loveday M, Grant AD, Moshabela M, Kielmann K, Nicol MP. The role of emergent champions in policy implementation for decentralised drug-resistant tuberculosis care in South Africa. BMJ Glob Health 2022; 7:bmjgh-2022-008907. [PMID: 36593649 PMCID: PMC9743276 DOI: 10.1136/bmjgh-2022-008907] [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: 02/24/2022] [Accepted: 11/07/2022] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE Champions are recognised as important to driving organisational change in healthcare quality improvement initiatives in high-income settings. In low-income and middle-income countries with a high disease burden and constrained human resources, their role is highly relevant yet understudied. Within a broader study on policy implementation for decentralised drug-resistant tuberculosis care in South Africa, we characterised the role, strategies and organisational context of emergent policy champions. DESIGN Interviews with 34 healthcare workers in three South African provinces identified the presence of individuals who had a strong influence on driving policy implementation forward. Additional interviews were conducted with 13 participants who were either identified as champions in phase II or were healthcare workers in facilities in which the champions operated. Thematic analyses using a socio-ecological framework further explored their strategies and the factors enabling or obstructing their agency. RESULTS All champions occupied senior managerial posts and were accorded legitimacy and authority by their communities. 'Disease-centred' champions had a high level of clinical expertise and placed emphasis on clinical governance and clinical outcomes, while 'patient-centred' champions promoted pathways of care that would optimise patients' recovery while minimising disruption in other spheres of their lives. Both types of champions displayed high levels of resourcefulness and flexibility to adapt strategies to the resource-constrained organisational context. CONCLUSION Policymakers can learn from champions' experiences regarding barriers and enablers to implementation to adapt policy. Research is needed to understand what factors can promote the sustainability of champion-led policy implementation, and to explore best management practices to support their initiatives.
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Affiliation(s)
- Sacha Roxanne Le Roux
- Division of Medical Microbiology,Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Waasila Jassat
- School of Public Health, University of the Western Cape, Cape Town, South Africa
| | - Lindy Dickson
- Division of Medical Microbiology,Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Leila Mitrani
- Division of Medical Microbiology,Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Helen Cox
- Division of Medical Microbiology,Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa,Institute for Infectious Disease and Molecular Medicine and Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
| | - Koleka Mlisana
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - John Black
- Division of Infectious Diseases, Department of Medicine, University of Cape Town, Cape Town, South Africa,Department of Infectious Diseases, Livingstone Hospital, Port Elizabeth, South Africa
| | - Marian Loveday
- South Africa HIV and other Infectious Diseases Research Unit, South African Medical Research Council, Durban, South Africa,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Alison D Grant
- TB Centre, London School of Hygiene & Tropical Medicine, London, UK,Africa Health Research Institute, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa,School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Mosa Moshabela
- School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Karina Kielmann
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium,Institute of Global Health and Development, Queen Margaret University, Edinburgh, UK
| | - Mark P Nicol
- Division of Medical Microbiology,Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa,Infection and Immunity, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
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21
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Tlotleng N, Cohen C, Made F, Kootbodien T, Masha M, Naicker N, Blumberg L, Jassat W. COVID-19 hospital admissions and mortality among healthcare workers in South Africa, 2020-2021. IJID Reg 2022; 5:54-61. [PMID: 36065332 PMCID: PMC9433333 DOI: 10.1016/j.ijregi.2022.08.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/30/2022]
Abstract
Objectives This study describes the characteristics of admitted HCWs reported to the DATCOV surveillance system, and the factors associated with in-hospital mortality in South African HCWs. Methods Data from March 5, 2020 to April 30, 2021 were obtained from DATCOV, a national hospital surveillance system monitoring COVID-19 admissions in South Africa. Characteristics of HCWs were compared with those of non-HCWs. Furthermore, a logistic regression model was used to assess factors associated with in-hospital mortality among HCWs. Results In total, there were 169 678 confirmed COVID-19 admissions, of which 6364 (3.8%) were HCWs. More of these HCW admissions were accounted for in wave 1 (48.6%; n = 3095) than in wave 2 (32.0%; n = 2036). Admitted HCWs were less likely to be male (28.2%; n = 1791) (aOR 0.3; 95% CI 0.3-0.4), in the 50-59 age group (33.1%; n = 2103) (aOR 1.4; 95% CI 1.1-1.8), or accessing the private health sector (63.3%; n = 4030) (aOR 1.3; 95% CI 1.1-1.5). Age, comorbidities, race, wave, province, and sector were significant risk factors for COVID-19-related mortality. Conclusion The trends in cases showed a decline in HCW admissions in wave 2 compared with wave 1. Acquired SARS-COV-2 immunity from prior infection may have been a reason for reduced admissions and mortality of HCWs despite the more transmissible and more severe beta variant in wave 2.
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Affiliation(s)
- Nonhlanhla Tlotleng
- Epidemiology and Surveillance Section, National Institute for Occupational Health, National Health Laboratory Service, Braamfontein, Johannesburg 2001, South Africa
- Environmental Health Department, Faculty of Health Sciences, University of Johannesburg, Johannesburg 2028, South Africa
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Arcadia 0007, South Africa
| | - Cheryl Cohen
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Witwatersrand 2193, South Africa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Felix Made
- Epidemiology and Surveillance Section, National Institute for Occupational Health, National Health Laboratory Service, Braamfontein, Johannesburg 2001, South Africa
| | - Tahira Kootbodien
- Epidemiology and Surveillance Section, National Institute for Occupational Health, National Health Laboratory Service, Braamfontein, Johannesburg 2001, South Africa
| | - Maureen Masha
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Johannesburg, South Africa
- Right to Care, Johannesburg, South Africa
| | - Nisha Naicker
- Environmental Health Department, Faculty of Health Sciences, University of Johannesburg, Johannesburg 2028, South Africa
| | - Lucille Blumberg
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Johannesburg, South Africa
- Right to Care, Johannesburg, South Africa
| | - Waasila Jassat
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Johannesburg, South Africa
- Right to Care, Johannesburg, South Africa
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22
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Wulf Hanson S, Abbafati C, Aerts JG, Al-Aly Z, Ashbaugh C, Ballouz T, Blyuss O, Bobkova P, Bonsel G, Borzakova S, Buonsenso D, Butnaru D, Carter A, Chu H, De Rose C, Diab MM, Ekbom E, El Tantawi M, Fomin V, Frithiof R, Gamirova A, Glybochko PV, Haagsma JA, Haghjooy Javanmard S, Hamilton EB, Harris G, Heijenbrok-Kal MH, Helbok R, Hellemons ME, Hillus D, Huijts SM, Hultström M, Jassat W, Kurth F, Larsson IM, Lipcsey M, Liu C, Loflin CD, Malinovschi A, Mao W, Mazankova L, McCulloch D, Menges D, Mohammadifard N, Munblit D, Nekliudov NA, Ogbuoji O, Osmanov IM, Peñalvo JL, Petersen MS, Puhan MA, Rahman M, Rass V, Reinig N, Ribbers GM, Ricchiuto A, Rubertsson S, Samitova E, Sarrafzadegan N, Shikhaleva A, Simpson KE, Sinatti D, Soriano JB, Spiridonova E, Steinbeis F, Svistunov AA, Valentini P, van de Water BJ, van den Berg-Emons R, Wallin E, Witzenrath M, Wu Y, Xu H, Zoller T, Adolph C, Albright J, Amlag JO, Aravkin AY, Bang-Jensen BL, Bisignano C, Castellano R, Castro E, Chakrabarti S, Collins JK, Dai X, Daoud F, Dapper C, Deen A, Duncan BB, Erickson M, Ewald SB, Ferrari AJ, Flaxman AD, Fullman N, Gamkrelidze A, Giles JR, Guo G, Hay SI, He J, Helak M, Hulland EN, Kereselidze M, Krohn KJ, Lazzar-Atwood A, Lindstrom A, Lozano R, Malta DC, Månsson J, Mantilla Herrera AM, Mokdad AH, Monasta L, Nomura S, Pasovic M, Pigott DM, Reiner RC, Reinke G, Ribeiro ALP, Santomauro DF, Sholokhov A, Spurlock EE, Walcott R, Walker A, Wiysonge CS, Zheng P, Bettger JP, Murray CJL, Vos T. Estimated Global Proportions of Individuals With Persistent Fatigue, Cognitive, and Respiratory Symptom Clusters Following Symptomatic COVID-19 in 2020 and 2021. JAMA 2022; 328:1604-1615. [PMID: 36215063 PMCID: PMC9552043 DOI: 10.1001/jama.2022.18931] [Citation(s) in RCA: 281] [Impact Index Per Article: 140.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/25/2022] [Indexed: 01/14/2023]
Abstract
Importance Some individuals experience persistent symptoms after initial symptomatic SARS-CoV-2 infection (often referred to as Long COVID). Objective To estimate the proportion of males and females with COVID-19, younger or older than 20 years of age, who had Long COVID symptoms in 2020 and 2021 and their Long COVID symptom duration. Design, Setting, and Participants Bayesian meta-regression and pooling of 54 studies and 2 medical record databases with data for 1.2 million individuals (from 22 countries) who had symptomatic SARS-CoV-2 infection. Of the 54 studies, 44 were published and 10 were collaborating cohorts (conducted in Austria, the Faroe Islands, Germany, Iran, Italy, the Netherlands, Russia, Sweden, Switzerland, and the US). The participant data were derived from the 44 published studies (10 501 hospitalized individuals and 42 891 nonhospitalized individuals), the 10 collaborating cohort studies (10 526 and 1906), and the 2 US electronic medical record databases (250 928 and 846 046). Data collection spanned March 2020 to January 2022. Exposures Symptomatic SARS-CoV-2 infection. Main Outcomes and Measures Proportion of individuals with at least 1 of the 3 self-reported Long COVID symptom clusters (persistent fatigue with bodily pain or mood swings; cognitive problems; or ongoing respiratory problems) 3 months after SARS-CoV-2 infection in 2020 and 2021, estimated separately for hospitalized and nonhospitalized individuals aged 20 years or older by sex and for both sexes of nonhospitalized individuals younger than 20 years of age. Results A total of 1.2 million individuals who had symptomatic SARS-CoV-2 infection were included (mean age, 4-66 years; males, 26%-88%). In the modeled estimates, 6.2% (95% uncertainty interval [UI], 2.4%-13.3%) of individuals who had symptomatic SARS-CoV-2 infection experienced at least 1 of the 3 Long COVID symptom clusters in 2020 and 2021, including 3.2% (95% UI, 0.6%-10.0%) for persistent fatigue with bodily pain or mood swings, 3.7% (95% UI, 0.9%-9.6%) for ongoing respiratory problems, and 2.2% (95% UI, 0.3%-7.6%) for cognitive problems after adjusting for health status before COVID-19, comprising an estimated 51.0% (95% UI, 16.9%-92.4%), 60.4% (95% UI, 18.9%-89.1%), and 35.4% (95% UI, 9.4%-75.1%), respectively, of Long COVID cases. The Long COVID symptom clusters were more common in women aged 20 years or older (10.6% [95% UI, 4.3%-22.2%]) 3 months after symptomatic SARS-CoV-2 infection than in men aged 20 years or older (5.4% [95% UI, 2.2%-11.7%]). Both sexes younger than 20 years of age were estimated to be affected in 2.8% (95% UI, 0.9%-7.0%) of symptomatic SARS-CoV-2 infections. The estimated mean Long COVID symptom cluster duration was 9.0 months (95% UI, 7.0-12.0 months) among hospitalized individuals and 4.0 months (95% UI, 3.6-4.6 months) among nonhospitalized individuals. Among individuals with Long COVID symptoms 3 months after symptomatic SARS-CoV-2 infection, an estimated 15.1% (95% UI, 10.3%-21.1%) continued to experience symptoms at 12 months. Conclusions and Relevance This study presents modeled estimates of the proportion of individuals with at least 1 of 3 self-reported Long COVID symptom clusters (persistent fatigue with bodily pain or mood swings; cognitive problems; or ongoing respiratory problems) 3 months after symptomatic SARS-CoV-2 infection.
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Affiliation(s)
- Sarah Wulf Hanson
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Cristiana Abbafati
- Department of Juridical and Economic Studies, La Sapienza University, Rome, Italy
| | - Joachim G Aerts
- Department of Pulmonary Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ziyad Al-Aly
- John T. Milliken Department of Internal Medicine, Washington University in St Louis, St Louis, Missouri
- Clinical Epidemiology Center, US Department of Veterans Affairs, St Louis, Missouri
| | - Charlie Ashbaugh
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Tala Ballouz
- Epidemiology, Biostatistics, and Prevention Institute, University of Zürich, Zurich, Switzerland
| | - Oleg Blyuss
- Wolfson Institute of Population Health, Queen Mary University of London, London, England
- Department of Pediatrics and Pediatric Infectious Diseases, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Polina Bobkova
- Clinical Medicine (Pediatric Profile), I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Gouke Bonsel
- EuroQol Research Foundation, Rotterdam, the Netherlands
| | - Svetlana Borzakova
- Pirogov Russian National Research Medical University, Moscow
- Research Institute for Healthcare Organization and Medical Management, Moscow Healthcare Department, Moscow, Russia
| | - Danilo Buonsenso
- Department of Woman and Child Health and Public Health, Agostino Gemelli University Polyclinic IRCCS, Rome, Italy
- Global Health Research Institute, Catholic University of Sacred Heart, Rome, Italy
| | - Denis Butnaru
- I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Austin Carter
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Helen Chu
- Department of Medicine, University of Washington, Seattle
| | - Cristina De Rose
- Department of Woman and Child Health and Public Health, Agostino Gemelli University Polyclinic IRCCS, Rome, Italy
| | - Mohamed Mustafa Diab
- Center for Policy Impact in Global Health, Duke University, Durham, North Carolina
- Department of Surgery, Duke University, Durham, North Carolina
| | - Emil Ekbom
- Uppsala University Hospital, Uppsala, Sweden
| | - Maha El Tantawi
- Pediatric Dentistry and Dental Public Health Department, Alexandria University, Alexandria, Egypt
| | - Victor Fomin
- Rector's Office, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Robert Frithiof
- Department of Surgical Sciences, Anesthesiology, and Intensive Care Medicine, Uppsala University, Uppsala, Sweden
| | - Aysylu Gamirova
- Clinical Medicine (General Medicine Profile), I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Petr V Glybochko
- Administration Department, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Juanita A Haagsma
- Department of Public Health, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Shaghayegh Haghjooy Javanmard
- Applied Physiology Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Erin B Hamilton
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | | | - Majanka H Heijenbrok-Kal
- Department of Rehabilitation Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
- Neurorehabilitation, Rijndam Rehabilitation, Rotterdam, the Netherlands
| | - Raimund Helbok
- Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
| | - Merel E Hellemons
- Department of Pulmonary Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - David Hillus
- Department of Infectious Diseases and Respiratory Medicine, Charité Medical University Berlin, Berlin, Germany
| | - Susanne M Huijts
- Department of Respiratory Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Michael Hultström
- Department of Surgical Sciences, Anesthesiology, and Intensive Care Medicine, Uppsala University, Uppsala, Sweden
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Waasila Jassat
- Department of Public Health Surveillance and Response, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité University Medical Center Berlin, Berlin, Germany
- Department of Clinical Research and Tropical Medicine, Bernhard-Nocht Institute of Tropical Medicine, Hamburg, Germany
| | - Ing-Marie Larsson
- Department of Surgical Sciences, Anesthesiology, and Intensive Care Medicine, Uppsala University, Uppsala, Sweden
| | - Miklós Lipcsey
- Department of Surgical Sciences, Anesthesiology, and Intensive Care Medicine, Uppsala University, Uppsala, Sweden
| | - Chelsea Liu
- Department of Epidemiology, Harvard University, Boston, Massachusetts
| | | | | | - Wenhui Mao
- Center for Policy Impact in Global Health, Duke University, Durham, North Carolina
- Duke Global Health Institute, Duke University, Durham, North Carolina
| | - Lyudmila Mazankova
- Russian Medical Academy of Continuous Professional Education, Ministry of Healthcare of the Russian Federation, Moscow
| | | | - Dominik Menges
- Epidemiology, Biostatistics, and Prevention Institute, University of Zürich, Zurich, Switzerland
| | - Noushin Mohammadifard
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Daniel Munblit
- Department of Pediatrics and Pediatric Infectious Diseases, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
- National Heart and Lung Institute, Imperial College London, London, England
| | - Nikita A Nekliudov
- Clinical Medicine (General Medicine Profile), I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Osondu Ogbuoji
- Duke Global Health Institute, Duke University, Durham, North Carolina
| | - Ismail M Osmanov
- Pirogov Russian National Research Medical University, Moscow
- ZA Bashlyaeva Children's Municipal Clinical Hospital, Moscow, Russia
| | - José L Peñalvo
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, Massachusetts
| | - Maria Skaalum Petersen
- Department of Occupational Medicine and Public Health, Faroese Hospital System, Torshavn, Faroe Islands
- Centre of Health Science, University of Faroe Islands, Torshavn
| | - Milo A Puhan
- Epidemiology, Biostatistics, and Prevention Institute, University of Zürich, Zurich, Switzerland
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland
| | - Mujibur Rahman
- Department of Internal Medicine, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Verena Rass
- Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
| | - Nickolas Reinig
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Gerard M Ribbers
- Department of Rehabilitation Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Antonia Ricchiuto
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Sten Rubertsson
- Department of Surgical Sciences, Anesthesiology, and Intensive Care Medicine, Uppsala University, Uppsala, Sweden
- Department of Surgical Sciences, Hedenstierna Laboratory, Uppsala University, Uppsala, Sweden
| | - Elmira Samitova
- Russian Medical Academy of Continuous Professional Education, Ministry of Healthcare of the Russian Federation, Moscow
- ZA Bashlyaeva Children's Municipal Clinical Hospital, Moscow, Russia
| | - Nizal Sarrafzadegan
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Anastasia Shikhaleva
- Clinical Medicine (Pediatric Profile), I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Kyle E Simpson
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Dario Sinatti
- Department of Woman and Child Health and Public Health, Agostino Gemelli University Polyclinic IRCCS, Rome, Italy
| | - Joan B Soriano
- Hospital Universitario de La Princesa, Madrid, Spain
- Centro de Investigación Biomédica en Red Enfermedades Respiratorias (Center for Biomedical Research in Respiratory Diseases Network), Madrid, Spain
| | - Ekaterina Spiridonova
- Clinical Medicine (General Medicine Profile), I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Fridolin Steinbeis
- Department of Infectious Diseases and Respiratory Medicine, Charité Medical University Berlin, Berlin, Germany
| | - Andrey A Svistunov
- Administration Department, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Piero Valentini
- Department of Woman and Child Health and Public Health, Agostino Gemelli University Polyclinic IRCCS, Rome, Italy
| | - Brittney J van de Water
- Department of Global Health and Social Medicine, Harvard University, Boston, Massachusetts
- Nursing and Midwifery Department, Seed Global Health, Boston, Massachusetts
| | - Rita van den Berg-Emons
- Department of Rehabilitation Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ewa Wallin
- Department of Surgical Sciences, Anesthesiology, and Intensive Care Medicine, Uppsala University, Uppsala, Sweden
| | - Martin Witzenrath
- Department of Infectious Diseases and Respiratory Medicine, Charité University Medical Center Berlin, Berlin, Germany
- German Center for Lung Research, Berlin
| | - Yifan Wu
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Hanzhang Xu
- Department of Family Medicine and Community Health, Duke University, Durham, North Carolina
| | - Thomas Zoller
- Department of Infectious Diseases and Respiratory Medicine, Charité Medical University Berlin, Berlin, Germany
| | - Christopher Adolph
- Department of Political Science, University of Washington, Seattle
- Center for Statistics and the Social Sciences, University of Washington, Seattle
| | - James Albright
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Joanne O Amlag
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Aleksandr Y Aravkin
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
- Department of Applied Mathematics, University of Washington, Seattle
- Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle
| | - Bree L Bang-Jensen
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Catherine Bisignano
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Rachel Castellano
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Emma Castro
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Suman Chakrabarti
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
- Department of Global Health, University of Washington, Seattle
| | - James K Collins
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Xiaochen Dai
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
- Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle
| | - Farah Daoud
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Carolyn Dapper
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Amanda Deen
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Bruce B Duncan
- Postgraduate Program in Epidemiology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Megan Erickson
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Samuel B Ewald
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Alize J Ferrari
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
- School of Public Health, University of Queensland, Brisbane, Australia
| | - Abraham D Flaxman
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
- Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle
| | - Nancy Fullman
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | | | - John R Giles
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Gaorui Guo
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Simon I Hay
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
- Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle
| | - Jiawei He
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Monika Helak
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Erin N Hulland
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
- Department of Global Health, University of Washington, Seattle
| | - Maia Kereselidze
- National Center for Disease Control and Public Health, Tbilisi, Georgia
| | - Kris J Krohn
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Alice Lazzar-Atwood
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Akiaja Lindstrom
- School of Public Health, University of Queensland, Brisbane, Australia
- School of Public Health, Queensland Centre for Mental Health Research, Wacol, Australia
| | - Rafael Lozano
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
- Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle
| | - Deborah Carvalho Malta
- Department of Maternal and Child Nursing and Public Health, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Johan Månsson
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Ana M Mantilla Herrera
- School of Public Health, University of Queensland, Brisbane, Australia
- West Moreton Hospital Health Services, Queensland Centre for Mental Health Research, Wacol, Australia
| | - Ali H Mokdad
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
- Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle
| | - Lorenzo Monasta
- Clinical Epidemiology and Public Health Research Unit, Burlo Garofolo Institute for Maternal and Child Health, Trieste, Italy
| | - Shuhei Nomura
- Department of Health Policy and Management, Keio University, Tokyo, Japan
- Department of Global Health Policy, University of Tokyo, Tokyo, Japan
| | - Maja Pasovic
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - David M Pigott
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
- Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle
| | - Robert C Reiner
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
- Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle
| | - Grace Reinke
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Antonio Luiz P Ribeiro
- Department of Internal Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Centre of Telehealth, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Damian Francesco Santomauro
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
- School of Public Health, University of Queensland, Brisbane, Australia
- Policy and Epidemiology Group, Queensland Centre for Mental Health Research, Wacol, Australia
| | - Aleksei Sholokhov
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Emma Elizabeth Spurlock
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
- Department of Social and Behavioral Sciences, School of Public Health, Yale University, New Haven, Connecticut
| | - Rebecca Walcott
- Evans School of Public Policy and Governance, University of Washington, Seattle
| | - Ally Walker
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Charles Shey Wiysonge
- Cochrane South Africa, South African Medical Research Council, Cape Town
- HIV and Other Infectious Diseases Research Unit, South African Medical Research Council, Durban
| | - Peng Zheng
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
- Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle
| | - Janet Prvu Bettger
- Department of Orthopedic Surgery, Duke University, Durham, North Carolina
| | - Christopher J L Murray
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
- Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle
| | - Theo Vos
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
- Department of Health Metrics Sciences, School of Medicine, University of Washington, Seattle
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Gonçalves BP, Hall M, Jassat W, Balan V, Murthy S, Kartsonaki C, Semple MG, Rojek A, Baruch J, Reyes LF, Dasgupta A, Dunning J, Citarella BW, Pritchard M, Martín-Quiros A, Sili U, Baillie JK, Aryal D, Arabi Y, Rashan A, Angheben A, Caoili J, Carrier FM, Harrison EM, Gómez-Junyent J, Figueiredo-Mello C, Douglas JJ, Mat Nor MB, Chow YP, Wong XC, Bertagnolio S, Thwin SS, Streinu-Cercel A, Salazar L, Rishu A, Rangappa R, Ong DSY, Hashmi M, Carson G, Diaz J, Fowler R, Kraemer MUG, Wils EJ, Horby P, Merson L, Olliaro PL. An international observational study to assess the impact of the Omicron variant emergence on the clinical epidemiology of COVID-19 in hospitalised patients. eLife 2022; 11:e80556. [PMID: 36197074 PMCID: PMC9534549 DOI: 10.7554/elife.80556] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 05/25/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
Background Whilst timely clinical characterisation of infections caused by novel SARS-CoV-2 variants is necessary for evidence-based policy response, individual-level data on infecting variants are typically only available for a minority of patients and settings. Methods Here, we propose an innovative approach to study changes in COVID-19 hospital presentation and outcomes after the Omicron variant emergence using publicly available population-level data on variant relative frequency to infer SARS-CoV-2 variants likely responsible for clinical cases. We apply this method to data collected by a large international clinical consortium before and after the emergence of the Omicron variant in different countries. Results Our analysis, that includes more than 100,000 patients from 28 countries, suggests that in many settings patients hospitalised with Omicron variant infection less often presented with commonly reported symptoms compared to patients infected with pre-Omicron variants. Patients with COVID-19 admitted to hospital after Omicron variant emergence had lower mortality compared to patients admitted during the period when Omicron variant was responsible for only a minority of infections (odds ratio in a mixed-effects logistic regression adjusted for likely confounders, 0.67 [95% confidence interval 0.61-0.75]). Qualitatively similar findings were observed in sensitivity analyses with different assumptions on population-level Omicron variant relative frequencies, and in analyses using available individual-level data on infecting variant for a subset of the study population. Conclusions Although clinical studies with matching viral genomic information should remain a priority, our approach combining publicly available data on variant frequency and a multi-country clinical characterisation dataset with more than 100,000 records allowed analysis of data from a wide range of settings and novel insights on real-world heterogeneity of COVID-19 presentation and clinical outcome. Funding Bronner P. Gonçalves, Peter Horby, Gail Carson, Piero L. Olliaro, Valeria Balan, Barbara Wanjiru Citarella, and research costs were supported by the UK Foreign, Commonwealth and Development Office (FCDO) and Wellcome [215091/Z/18/Z, 222410/Z/21/Z, 225288/Z/22/Z]; and Janice Caoili and Madiha Hashmi were supported by the UK FCDO and Wellcome [222048/Z/20/Z]. Peter Horby, Gail Carson, Piero L. Olliaro, Kalynn Kennon and Joaquin Baruch were supported by the Bill & Melinda Gates Foundation [OPP1209135]; Laura Merson was supported by University of Oxford's COVID-19 Research Response Fund - with thanks to its donors for their philanthropic support. Matthew Hall was supported by a Li Ka Shing Foundation award to Christophe Fraser. Moritz U.G. Kraemer was supported by the Branco Weiss Fellowship, Google.org, the Oxford Martin School, the Rockefeller Foundation, and the European Union Horizon 2020 project MOOD (#874850). The contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views of the European Commission. Contributions from Srinivas Murthy, Asgar Rishu, Rob Fowler, James Joshua Douglas, François Martin Carrier were supported by CIHR Coronavirus Rapid Research Funding Opportunity OV2170359 and coordinated out of Sunnybrook Research Institute. Contributions from Evert-Jan Wils and David S.Y. Ong were supported by a grant from foundation Bevordering Onderzoek Franciscus; and Andrea Angheben by the Italian Ministry of Health "Fondi Ricerca corrente-L1P6" to IRCCS Ospedale Sacro Cuore-Don Calabria. The data contributions of J.Kenneth Baillie, Malcolm G. Semple, and Ewen M. Harrison were supported by grants from the National Institute for Health Research (NIHR; award CO-CIN-01), the Medical Research Council (MRC; grant MC_PC_19059), and by the NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool in partnership with Public Health England (PHE) (award 200907), NIHR HPRU in Respiratory Infections at Imperial College London with PHE (award 200927), Liverpool Experimental Cancer Medicine Centre (grant C18616/A25153), NIHR Biomedical Research Centre at Imperial College London (award IS-BRC-1215-20013), and NIHR Clinical Research Network providing infrastructure support. All funders of the ISARIC Clinical Characterisation Group are listed in the appendix.
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Affiliation(s)
- Bronner P Gonçalves
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Waasila Jassat
- National Institute for Communicable Diseases, South Africa; Right to CareJohannesburgSouth Africa
| | - Valeria Balan
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
| | - Srinivas Murthy
- Faculty of Medicine, University of British ColumbiaVancouverCanada
| | - Christiana Kartsonaki
- MRC Population Health Research Unit, Clinical Trials Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of OxfordOxfordUnited Kingdom
| | - Malcolm G Semple
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of LiverpoolLiverpoolUnited Kingdom
- Respiratory Medicine, Alder Hey Children's Hospital, University of LiverpoolLiverpoolUnited Kingdom
| | - Amanda Rojek
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
- Royal Melbourne HospitalMelbourneAustralia
- Centre for Integrated Critical Care, University of MelbourneMelbourneAustralia
| | - Joaquín Baruch
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
| | - Luis Felipe Reyes
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
- Universidad de La SabanaChiaColombia
- Clinica Universidad de La SabanaChiaColombia
| | - Abhishek Dasgupta
- Department of Computer Science, University of OxfordOxfordUnited Kingdom
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | - Jake Dunning
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
| | | | - Mark Pritchard
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
| | | | - Uluhan Sili
- Department of Infectious Diseases and Clinical Microbiology, School of Medicine, Marmara UniversityIstanbulTurkey
| | - J Kenneth Baillie
- Roslin Institute, University of EdinburghEdinburghUnited Kingdom
- Intensive Care Unit, Royal Infirmary of EdinburghEdinburghUnited Kingdom
| | - Diptesh Aryal
- Critical Care and Anesthesia, Nepal Mediciti HospitalLalitpurNepal
| | - Yaseen Arabi
- King Abdullah International Medical Research Center and King Saud Bin Abdulaziz University for Health SciencesRiyadhSaudi Arabia
| | - Aasiyah Rashan
- Network for Improving Critical care Systems and TrainingColomboSri Lanka
| | - Andrea Angheben
- Department of Infectious, Tropical Diseases and Microbiology (DITM), IRCCS Sacro Cuore Don Calabria Hospital, Negrar di ValpolicellaVeronaItaly
| | | | - François Martin Carrier
- Department of Anesthesiology, Centre hospitalier de l'Université de MontréalMontréalCanada
- Department of Medicine, Critical Care Division, Centre hospitalier de l'Université de MontréalMontréalCanada
- Carrefour de l'innovation et santé des populations, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM)MontréalCanada
- Department of Anesthesiology and Pain Medicine, Université de MontréalMontréalCanada
| | - Ewen M Harrison
- Centre for Medical Informatics, The University of Edinburgh, Usher Institute of Population Health Sciences and InformaticsEdinburghUnited Kingdom
| | - Joan Gómez-Junyent
- Department of Infectious Diseases, Hospital del Mar, Infectious Pathology and Antimicrobial Research Group (IPAR), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu FabraBarcelonaSpain
| | | | | | | | - Yock Ping Chow
- Clinical Research Centre, Sunway Medical Centre, Selangor Darul EhsanSelangorMalaysia
| | - Xin Ci Wong
- Digital Health Research and Innovation Unit, Institute for Clinical Research, National Institutes of Health (NIH)SelangorMalaysia
| | | | | | - Anca Streinu-Cercel
- Carol Davila University of Medicine and PharmacyBucharestRomania
- National Institute for Infectious Diseases "Prof. Dr. Matei Bals"BucharestRomania
| | | | - Asgar Rishu
- Department of Critical Care Medicine, Sunnybrook Health Sciences CentreTorontoCanada
| | | | - David SY Ong
- Department of Medical Microbiology and Infection Control, Franciscus Gasthuis & VlietlandRotterdamNetherlands
| | - Madiha Hashmi
- Critical Care Asia and Ziauddin UniversityKarachiPakistan
| | - Gail Carson
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
| | - Janet Diaz
- World Health OrganizationGenèveSwitzerland
| | - Rob Fowler
- Department of Critical Care Medicine, Sunnybrook Health Sciences CentreTorontoCanada
| | - Moritz UG Kraemer
- Department of Biology, University of OxfordOxfordUnited Kingdom
- Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
| | - Evert-Jan Wils
- Department of Intensive Care, Franciscus Gasthuis & VlietlandRotterdamNetherlands
| | - Peter Horby
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
| | - Laura Merson
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
- Infectious Diseases Data Observatory, Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
| | - Piero L Olliaro
- ISARIC, Pandemic Sciences Institute, University of OxfordOxfordUnited Kingdom
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24
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Reichert E, Schaeffer B, Gantt S, Rumpler E, Govender N, Welch R, Shonhiwa AM, Iwu CD, Lamola TM, Moema-Matiea I, Muganhiri D, Hanage W, Santillana M, Jassat W, Cohen C, Swerdlow D. Methods for early characterisation of the severity and dynamics of SARS-CoV-2 variants: a population-based time series analysis in South Africa. Lancet Microbe 2022; 3:e753-e761. [PMID: 36057266 PMCID: PMC9432868 DOI: 10.1016/s2666-5247(22)00182-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/23/2022] [Accepted: 06/13/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Assessment of disease severity associated with a novel pathogen or variant provides crucial information needed by public health agencies and governments to develop appropriate responses. The SARS-CoV-2 omicron variant of concern (VOC) spread rapidly through populations worldwide before robust epidemiological and laboratory data were available to investigate its relative severity. Here we develop a set of methods that make use of non-linked, aggregate data to promptly estimate the severity of a novel variant, compare its characteristics with those of previous VOCs, and inform data-driven public health responses. METHODS Using daily population-level surveillance data from the National Institute for Communicable Diseases in South Africa (March 2, 2020, to Jan 28, 2022), we determined lag intervals most consistent with time from case ascertainment to hospital admission and within-hospital death through optimisation of the distance correlation coefficient in a time series analysis. We then used these intervals to estimate and compare age-stratified case-hospitalisation and case-fatality ratios across the four epidemic waves that South Africa has faced, each dominated by a different variant. FINDINGS A total of 3 569 621 cases, 494 186 hospitalisations, and 99 954 deaths attributable to COVID-19 were included in the analyses. We found that lag intervals and disease severity were dependent on age and variant. At an aggregate level, fluctuations in cases were generally followed by a similar trend in hospitalisations within 7 days and deaths within 15 days. We noted a marked reduction in disease severity throughout the omicron period relative to previous waves (age-standardised case-fatality ratios were consistently reduced by >50%), most substantial for age strata with individuals 50 years or older. INTERPRETATION This population-level time series analysis method, which calculates an optimal lag interval that is then used to inform the numerator of severity metrics including the case-hospitalisation and case-fatality ratio, provides useful and timely estimates of the relative effects of novel SARS-CoV-2 VOCs, especially for application in settings where resources are limited. FUNDING National Institute for Communicable Diseases of South Africa, South African National Government.
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Affiliation(s)
- Emily Reichert
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Correspondence to: Emily Reichert, Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Beau Schaeffer
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Shae Gantt
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Eva Rumpler
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Nevashan Govender
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Richard Welch
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Andronica Moipone Shonhiwa
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Chidozie Declan Iwu
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Teresa Mashudu Lamola
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Itumeleng Moema-Matiea
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Darren Muganhiri
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - William Hanage
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mauricio Santillana
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Waasila Jassat
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, 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
| | - David Swerdlow
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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25
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Marwali EM, Kekalih A, Yuliarto S, Wati DK, Rayhan M, Valerie IC, Cho HJ, Jassat W, Blumberg L, Masha M, Semple C, Swann OV, Kohns Vasconcelos M, Popielska J, Murthy S, Fowler RA, Guerguerian AM, Streinu-Cercel A, Pathmanathan MD, Rojek A, Kartsonaki C, Gonçalves BP, Citarella BW, Merson L, Olliaro PL, Dalton HJ. Paediatric COVID-19 mortality: a database analysis of the impact of health resource disparity. BMJ Paediatr Open 2022; 6:e001657. [PMID: 36645791 PMCID: PMC9621167 DOI: 10.1136/bmjpo-2022-001657] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/07/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND The impact of the COVID-19 pandemic on paediatric populations varied between high-income countries (HICs) versus low-income to middle-income countries (LMICs). We sought to investigate differences in paediatric clinical outcomes and identify factors contributing to disparity between countries. METHODS The International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC) COVID-19 database was queried to include children under 19 years of age admitted to hospital from January 2020 to April 2021 with suspected or confirmed COVID-19 diagnosis. Univariate and multivariable analysis of contributing factors for mortality were assessed by country group (HICs vs LMICs) as defined by the World Bank criteria. RESULTS A total of 12 860 children (3819 from 21 HICs and 9041 from 15 LMICs) participated in this study. Of these, 8961 were laboratory-confirmed and 3899 suspected COVID-19 cases. About 52% of LMICs children were black, and more than 40% were infants and adolescent. Overall in-hospital mortality rate (95% CI) was 3.3% [=(3.0% to 3.6%), higher in LMICs than HICs (4.0% (3.6% to 4.4%) and 1.7% (1.3% to 2.1%), respectively). There were significant differences between country income groups in intervention profile, with higher use of antibiotics, antivirals, corticosteroids, prone positioning, high flow nasal cannula, non-invasive and invasive mechanical ventilation in HICs. Out of the 439 mechanically ventilated children, mortality occurred in 106 (24.1%) subjects, which was higher in LMICs than HICs (89 (43.6%) vs 17 (7.2%) respectively). Pre-existing infectious comorbidities (tuberculosis and HIV) and some complications (bacterial pneumonia, acute respiratory distress syndrome and myocarditis) were significantly higher in LMICs compared with HICs. On multivariable analysis, LMIC as country income group was associated with increased risk of mortality (adjusted HR 4.73 (3.16 to 7.10)). CONCLUSION Mortality and morbidities were higher in LMICs than HICs, and it may be attributable to differences in patient demographics, complications and access to supportive and treatment modalities.
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Affiliation(s)
- Eva Miranda Marwali
- Department of Pediatric Cardiac Intensive Care, National Cardiovascular Center Harapan Kita, Jakarta, Indonesia
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC), Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Aria Kekalih
- Department of Community Medicine, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Saptadi Yuliarto
- Department of Pediatrics, Faculty of Medicine, Universitas Brawijaya, Saiful Anwar Hospital, Malang, Jawa Timur, Indonesia
| | - Dyah Kanya Wati
- Department of Pediatrics, Faculty of Medicine, Universitas Udayana, Sanglah Hospital, Denpasar, Bali, Indonesia
| | - Muhammad Rayhan
- Department of Pediatric Cardiac Intensive Care, National Cardiovascular Center Harapan Kita, Jakarta, Indonesia
| | - Ivy Cerelia Valerie
- Department of Pediatrics, Faculty of Medicine, Universitas Udayana, Sanglah Hospital, Denpasar, Bali, Indonesia
| | - Hwa Jin Cho
- Division of Pediatric Cardiology and Pediatric Intensive Care, Department of Pediatrics, Chonnam National University Hospital, Gwangju, Korea (the Republic of)
| | - Waasila Jassat
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Lucille Blumberg
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Maureen Masha
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Calum Semple
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC), Pandemic Sciences Institute, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection Veterinary and Ecological Sciences, University of Liverpool, Liverpool, Merseyside, UK
| | - Olivia V Swann
- Centre for Medical Informatics, The University of Edinburgh Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | | | - Jolanta Popielska
- Warsaw's Hospital for Infectious Diseases, Medical University of Warsaw, Warszawa, Mazowieckie, Poland
| | - Srinivas Murthy
- Department of Pediatrics, Division of Critical Care, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert A Fowler
- Interdepartmental Division of Critical Care Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Anne-Marie Guerguerian
- Department of Critical Care Medicine, Neurosciences and Mental Health Program, Faculty of Medicine, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anca Streinu-Cercel
- National Institute of Infectious Diseases Prof Dr Matei Bals, Bucuresti, Romania
| | - Mohan Dass Pathmanathan
- National Institutes of Health, Ministry of Health Malaysia, Putrajaya, Wilayah Persekutuan, Malaysia
| | - Amanda Rojek
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC), Pandemic Sciences Institute, University of Oxford, Oxford, UK
- The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Christiana Kartsonaki
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC), Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Bronner P Gonçalves
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC), Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Barbara Wanjiru Citarella
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC), Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Laura Merson
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC), Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Piero L Olliaro
- International Severe Acute Respiratory and emerging Infection Consortium (ISARIC), Pandemic Sciences Institute, University of Oxford, Oxford, UK
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Sikhosana ML, Jassat W, Makatini Z. Characteristics of hospitalised COVID-19 patients during the first two pandemic waves, Gauteng. S Afr J Infect Dis 2022; 37:434. [PMID: 36254313 PMCID: PMC9557933 DOI: 10.4102/sajid.v37i1.434] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/25/2022] [Indexed: 11/05/2022] Open
Abstract
Background Gauteng province (GP) was one of the most affected provinces in the country during the first two pandemic waves in South Africa. We aimed to describe the characteristics of coronavirus disease 2019 (COVID-19) patients admitted in one of the largest quaternary hospitals in GP during the first two waves. Objectives Study objectives were to determine factors associated with hospital admission during the second wave and to describe factors associated with in-hospital COVID-19 mortality. Method Data from a national hospital-based surveillance system of COVID-19 hospitalisations were used. Multivariable logistic regression models were conducted to compare patients hospitalised during wave 1 and wave 2, and to determine factors associated with in-hospital mortality. Results The case fatality ratio was the highest (39.95%) during wave 2. Factors associated with hospitalisation included age groups 40–59 years (adjusted odds ratio [aOR]: 2.14, 95% confidence interval [CI]: 1.08–4.27), 60–79 years (aOR: 2.49, 95% CI: 1.23–5.02) and ≥ 80 years (aOR: 3.39, 95% CI: 1.35–8.49). Factors associated with in–hospital mortality included age groups 60–79 years (aOR: 2.55, 95% CI: 1.11–5.84) and ≥ 80 years (aOR: 5.66, 95% CI: 2.12–15.08); male sex (aOR: 1.56, 95% CI: 1.22–1.99); presence of an underlying comorbidity (aOR: 1.76, 95% CI: 1.37–2.26), as well as being admitted during post–wave 2 (aOR: 2.42, 95% CI: 1.33–4.42). Conclusion Compared to the recent omicron-driven pandemic waves characterised by lower admission rates and less disease severity among younger patients, COVID-19 in-hospital mortality during the earlier waves was associated with older age, being male and having an underlying comorbidity. Contribution This study showed how an active surveillance system can contribute towards identifying changes in disease trends.
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Affiliation(s)
- Mpho L. Sikhosana
- Department of Virology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Waasila Jassat
- Department of Public Health and Outbreak Response, National Institute of Communicable Diseases, Johannesburg, South Africa
| | - Zinhle Makatini
- Department of Virology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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27
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Dryden M, Mudara C, Vika C, Blumberg L, Mayet N, Cohen C, Tempia S, Parker A, Nel J, Perumal R, Groome MJ, Conradie F, Ndjeka N, Sigfrid L, Merson L, Jassat W. Post-COVID-19 condition 3 months after hospitalisation with SARS-CoV-2 in South Africa: a prospective cohort study. Lancet Glob Health 2022; 10:e1247-e1256. [PMID: 35961348 PMCID: PMC9363040 DOI: 10.1016/s2214-109x(22)00286-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Post COVID-19 condition (PCC), as defined by WHO, refers to a wide range of new, returning, or ongoing health problems in people who have had COVID-19, and it represents a rapidly emerging public health priority. We aimed to establish how this developing condition has affected patients in South Africa and which population groups are at risk. METHODS In this prospective cohort study, we used the DATCOV national hospital surveillance system to identify participants aged 18 years or older who had been hospitalised with laboratory-confirmed SARS-CoV-2 infection in South Africa. Participants underwent telephone follow-up assessment at 1 month and 3 months after hospital discharge. Participants were assessed using a standardised questionnaire for the evaluation of symptoms, functional status, health-related quality of life, and occupational status. We used negative binomial regression models to determine factors associated with PCC. FINDINGS Of 241 159 COVID-19 admissions reported to DATCOV between Dec 1, 2020, and Aug 23, 2021, 8309 were randomly selected for enrolment. Of the 3094 patients that we were able to contact, 2410 (77·9%) consented to participate in the study at 1 month after discharge. Of these, 1873 (77·7%) were followed up at 3 months after hospital discharge. Participants had a median age of 52 years (IQR 41-62) and 960 (51·3%) were women. At 3 months of follow-up, 1249 (66·7%) of 1873 participants reported new or persistent COVID-19-related symptoms, compared with 1978 (82·1%) of 2410 at 1 month after hospital discharge. The most common symptoms reported at 3 months were fatigue (50·3%), shortness of breath (23·4%), confusion or lack of concentration (17·5%), headaches (13·8%), and problems seeing or blurred vision (10·1%). On multivariable analysis, the factors associated with persistent symptoms after acute COVID-19 were being female (adjusted incident rate ratio 1·20, 95% CI 1·04-1·38) and admission to an intensive care unit (1·17, 1·01-1·37). INTERPRETATION Most participants in this cohort of individuals previously hospitalised with COVID-19 reported persistent symptoms 3 months after hospital discharge and a significant impact of PCC on their functional and occupational status. The large burden of PCC symptoms identified in this study emphasises the need for a national health strategy. This should include the development of clinical guidelines and training of health-care workers for identifying, assessing, and caring for patients affected by PCC; establishment of multidisciplinary health services; and provision of information and support to people who have PCC. FUNDING Bill & Melinda Gates Foundation, UK Foreign, Commonwealth & Development Office, and Wellcome.
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Affiliation(s)
- Murray Dryden
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Division of the National Health Laboratory Services, Johannesburg, South Africa.
| | - Caroline Mudara
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Division of the National Health Laboratory Services, Johannesburg, South Africa
| | - Caroline Vika
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Division of the National Health Laboratory Services, Johannesburg, South Africa
| | - Lucille Blumberg
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Division of the National Health Laboratory Services, Johannesburg, South Africa; Right to Care, Centurion, South Africa
| | - Natalie Mayet
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Division of the National Health Laboratory Services, Johannesburg, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Services, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Services, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Arifa Parker
- Divisions of General Medicine and Infectious Diseases, Faculty of Medicine and Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Jeremy Nel
- Department of Medicine, Division of Infectious Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Rubeshan Perumal
- South African Medical Research Council-CAPRISA HIV-Tuberculosis Pathogenesis and Treatment Research Unit, Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Michelle J Groome
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Division of the National Health Laboratory Services, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Francesca Conradie
- Clinical HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Norbert Ndjeka
- Drug-Resistant Tuberculosis, Tuberculosis & HIV Directorate, National Department of Health, Pretoria, South Africa and University of KwaZulu-Natal, Durban, South Africa
| | - Louise Sigfrid
- Global Support Centre, International Severe Acute Respiratory and emerging Infections Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Laura Merson
- Pandemic Sciences Centre, International Severe Acute Respiratory and emerging Infections Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Waasila Jassat
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Division of the National Health Laboratory Services, Johannesburg, South Africa; Right to Care, Centurion, South Africa
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28
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Wolter N, Tempia S, von Gottberg A, Bhiman JN, Walaza S, Kleynhans J, Moyes J, Buys A, McMorrow ML, Aitken S, Magni S, Yun J, Fellows T, Maakamedi T, Weiner R, Cawood C, Martinson N, Lebina L, Jassat W, Brauer M, Cohen C. Seroprevalence of Severe Acute Respiratory Syndrome Coronavirus 2 After the Second Wave in South Africa in Human Immunodeficiency Virus-Infected and Uninfected Persons: A Cross-Sectional Household Survey. Clin Infect Dis 2022; 75:e57-e68. [PMID: 35271693 PMCID: PMC9047164 DOI: 10.1093/cid/ciac198] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Seroprevalence studies are important for quantifying the burden of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in resource-constrained countries. METHODS We conducted a cross-sectional household survey spanning the second pandemic wave (November 2020 to April 2021) in 3 communities. Blood was collected for SARS-CoV-2 antibody (2 enzyme-linked immunosorbent assays targeting spike and nucleocapsid) and human immunodeficiency virus (HIV) testing. An individual was considered seropositive if testing positive on ≥1 assay. Factors associated with infection, and the age-standardized infection case detection rate, infection hospitalization rate, and infection fatality rate were calculated. RESULTS Overall, 7959 participants were enrolled, with a median age of 34 years and an HIV prevalence of 22.7%. SARS-CoV-2 seroprevalence was 45.2% (95% confidence interval 43.7%-46.7%) and increased from 26.9% among individuals enrolled in December 2020 to 47.1% among those enrolled in April 2021. On multivariable analysis, seropositivity was associated with age, sex, race, being overweight/obese, having respiratory symptoms, and low socioeconomic status. Persons living with HIV with high viral load were less likely to be seropositive than HIV-uninfected individuals. The site-specific infection case detection rate, infection hospitalization rate, and infection fatality rate ranged across sites from 4.4% to 8.2%, 1.2% to 2.5%, and 0.3% to 0.6%, respectively. CONCLUSIONS South Africa has experienced a large burden of SARS-CoV-2 infections, with <10% of infections diagnosed. Lower seroprevalence among persons living with HIV who are not virally suppressed, likely as a result of inadequate antibody production, highlights the need to prioritize this group for intervention.
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Affiliation(s)
- Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, 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
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GeorgiaUSA
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jinal N Bhiman
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, 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
| | - Jackie Kleynhans
- Centre for Respiratory Diseases and Meningitis, 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
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, 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
| | - Amelia Buys
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Meredith L McMorrow
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GeorgiaUSA
| | - Sue Aitken
- Genesis Analytics, Johannesburg, South Africa
| | - Sarah Magni
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genesis Analytics, Johannesburg, South Africa
| | - Jessica Yun
- Genesis Analytics, Johannesburg, South Africa
| | | | | | - Renay Weiner
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Neil Martinson
- Perinatal HIV Research Unit, MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, South Africa
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University Center for TB Research, Baltimore, Maryland, USA
| | - Limakatso Lebina
- Perinatal HIV Research Unit, MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, South Africa
| | - Waasila Jassat
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africaand
| | - Marieke Brauer
- Immunology Department, National Reference Laboratory, Ampath Pathology, Pretoria, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, 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
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Bingham J, Tempia S, Moultrie H, Viboud C, Jassat W, Cohen C, Pulliam JRC. Estimating the time-varying reproduction number for COVID-19 in South Africa during the first four waves using multiple measures of incidence for public and private sectors across four waves. medRxiv 2022:2022.07.22.22277932. [PMID: 35982666 PMCID: PMC9387150 DOI: 10.1101/2022.07.22.22277932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Objectives We aimed to quantify transmission trends in South Africa during the first four waves of the COVID-19 pandemic using estimates of the time-varying reproduction number (R) and to compare the robustness of R estimates based on three different data sources and using data from public and private sector service providers. Methods We estimated R from March 2020 through April 2022, nationally and by province, based on time series of rt-PCR-confirmed cases, hospitalizations, and hospital-associated deaths, using a method which models daily incidence as a weighted sum of past incidence. We also estimated R separately using public and private sector data. Results Nationally, the maximum case-based R following the introduction of lockdown measures was 1.55 (CI: 1.43-1.66), 1.56 (CI: 1.47-1.64), 1.46 (CI: 1.38-1.53) and 3.33 (CI: 2.84-3.97) during the first (Wuhan-Hu), second (Beta), third (Delta), and fourth (Omicron) waves respectively. Estimates based on the three data sources (cases, hospitalisations, deaths) were generally similar during the first three waves but case-based estimates were higher during the fourth wave. Public and private sector R estimates were generally similar except during the initial lockdowns and in case-based estimates during the fourth wave. Discussion Agreement between R estimates using different data sources during the first three waves suggests that data from any of these sources could be used in the early stages of a future pandemic. High R estimates for Omicron relative to earlier waves is interesting given a high level of exposure pre-Omicron. The agreement between public and private sector R estimates highlights the fact that clients of the public and private sectors did not experience two separate epidemics, except perhaps to a limited extent during the strictest lockdowns in the first wave.
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Affiliation(s)
- Jeremy Bingham
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Harry Moultrie
- Centre for Tuberculosis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cecile Viboud
- Fogarty International Center, NIH, Bethesda, MD, USA
| | - Waasila Jassat
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- Right to Care, Pretoria, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Juliet R C Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
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Wolter N, Jassat W, von Gottberg A, Cohen C. Clinical severity of omicron lineage BA.2 infection compared with BA.1 infection in South Africa. Lancet 2022; 400:93-96. [PMID: 35780802 PMCID: PMC9246473 DOI: 10.1016/s0140-6736(22)00981-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/07/2022] [Accepted: 05/24/2022] [Indexed: 12/15/2022]
Affiliation(s)
- Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Waasila Jassat
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; Right to Care, Centurion, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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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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Jassat W, Ozougwu L, Munshi S, Mudara C, Vika C, Arendse T, Masha M, Welch R, Govender N, Ebonwu J, Groome M, Joseph A, Madhi SA, Cohen C, Blumberg L. Corrigendum: The intersection of age, sex, race and socioeconomic status in COVID-19 hospital admissions and deaths in South Africa. S AFR J SCI 2022. [DOI: 10.17159/sajs.2022/13323c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Waasila Jassat
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Right to Care, Pretoria, South Africa
| | - Lovelyn Ozougwu
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Shehnaz Munshi
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Caroline Mudara
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Caroline Vika
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Tracy Arendse
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Maureen Masha
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Right to Care, Pretoria, South Africa
| | - Richard Welch
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Nevashan Govender
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Joy Ebonwu
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Michelle Groome
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Shabir A. Madhi
- South African Medical Research Council (SAMRC) Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- African Leadership in Vaccinology Expertise (ALIVE), University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Lucille Blumberg
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Right to Care, Pretoria, South Africa
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33
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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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Dheda K, Perumal T, Moultrie H, Perumal R, Esmail A, Scott AJ, Udwadia Z, Chang KC, Peter J, Pooran A, von Delft A, von Delft D, Martinson N, Loveday M, Charalambous S, Kachingwe E, Jassat W, Cohen C, Tempia S, Fennelly K, Pai M. The intersecting pandemics of tuberculosis and COVID-19: population-level and patient-level impact, clinical presentation, and corrective interventions. Lancet Respir Med 2022; 10:603-622. [PMID: 35338841 PMCID: PMC8942481 DOI: 10.1016/s2213-2600(22)00092-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 02/17/2022] [Accepted: 03/03/2022] [Indexed: 01/19/2023]
Abstract
The global tuberculosis burden remains substantial, with more than 10 million people newly ill per year. Nevertheless, tuberculosis incidence has slowly declined over the past decade, and mortality has decreased by almost a third in tandem. This positive trend was abruptly reversed by the COVID-19 pandemic, which in many parts of the world has resulted in a substantial reduction in tuberculosis testing and case notifications, with an associated increase in mortality, taking global tuberculosis control back by roughly 10 years. Here, we consider points of intersection between the tuberculosis and COVID-19 pandemics, identifying wide-ranging approaches that could be taken to reverse the devastating effects of COVID-19 on tuberculosis control. We review the impact of COVID-19 at the population level on tuberculosis case detection, morbidity and mortality, and the patient-level impact, including susceptibility to disease, clinical presentation, diagnosis, management, and prognosis. We propose strategies to reverse or mitigate the deleterious effects of COVID-19 and restore tuberculosis services. Finally, we highlight research priorities and major challenges and controversies that need to be addressed to restore and advance the global response to tuberculosis.
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Affiliation(s)
- Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and University of Cape Town Lung Institute, University of Cape Town, Cape Town, South Africa; South African Medical Research Council (SAMRC) Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
| | - Tahlia Perumal
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and University of Cape Town Lung Institute, University of Cape Town, Cape Town, South Africa; South African Medical Research Council (SAMRC) Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
| | - Harry Moultrie
- Centre for TB, National Institute for Communicable Diseases, Division of the National Health Laboratory Services, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Rubeshan Perumal
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and University of Cape Town Lung Institute, University of Cape Town, Cape Town, South Africa; SAMRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Aliasgar Esmail
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and University of Cape Town Lung Institute, University of Cape Town, Cape Town, South Africa; South African Medical Research Council (SAMRC) Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
| | - Alex J Scott
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and University of Cape Town Lung Institute, University of Cape Town, Cape Town, South Africa; South African Medical Research Council (SAMRC) Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
| | - Zarir Udwadia
- Department of Pulmonology, P D Hinduja Hospital and Medical Research Centre, Mumbai, India
| | - Kwok Chiu Chang
- Tuberculosis and Chest Service, Department of Health, Hong Kong Special Administrative Region, China
| | - Jonathan Peter
- Allergy and Immunology unit, Division of Allergy and Clinical Immunology, University of Cape Town Lung Institute, University of Cape Town, Cape Town, South Africa
| | - Anil Pooran
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and University of Cape Town Lung Institute, University of Cape Town, Cape Town, South Africa; South African Medical Research Council (SAMRC) Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
| | - Arne von Delft
- School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa; TB Proof, Cape Town, South Africa
| | | | - Neil Martinson
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Johns Hopkins University Center for TB Research, Baltimore, MD, USA
| | - Marian Loveday
- HIV Prevention Research Unit, South African Medical Research Council, Durban, South Africa
| | - Salome Charalambous
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; The Aurum Institute, Johannesburg, South Africa
| | - Elizabeth Kachingwe
- Centre for TB, National Institute for Communicable Diseases, Division of the National Health Laboratory Services, Johannesburg, South Africa
| | - Waasila Jassat
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Cheryl Cohen
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Stefano Tempia
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Kevin Fennelly
- Pulmonary Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Madhukar Pai
- McGill International TB Centre, McGill University, Montreal, QC, Canada
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Jassat W, Ozougwu L, Munshi S, Mudara C, Vika C, Arendse T, Masha M, Welch R, Govender N, Ebonwu J, Groome M, Joseph A, Madhi SA, Cohen C, Blumberg L. The intersection of age, sex, race and socioeconomic status in COVID-19 hospital admissions and deaths in South Africa. S AFR J SCI 2022. [DOI: 10.17159/sajs.2022/13323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Older age, male sex, and non-white race have been reported to be risk factors for COVID-19 mortality. Few studies have explored how these intersecting factors contribute to COVID-19 outcomes. This study aimed to compare demographic characteristics and trends in SARS-CoV-2 admissions and the health care they received. Hospital admission data were collected through DATCOV, an active national COVID-19 surveillance programme. Descriptive analysis was used to compare admissions and deaths by age, sex, race, and health sector as a proxy for socio-economic status. COVID-19 mortality and healthcare utilisation were compared by race using random effect multivariable logistic regression models. On multivariable analysis, black African patients (adjusted OR [aOR] 1.3, 95% confidence interval [CI] 1.2, 1.3), coloured patients (aOR 1.2, 95% CI 1.1, 1.3), and patients of Indian descent (aOR 1.2, 95% CI 1.2, 1.3) had increased risk of in-hospital COVID-19 mortality compared to white patients; and admission in the public health sector (aOR 1.5, 95% CI 1.5, 1.6) was associated with increased risk of mortality compared to those in the private sector. There were higher percentages of COVID-19 hospitalised individuals treated in ICU, ventilated, and treated with supplemental oxygen in the private compared to the public sector. There were increased odds of non-white patients being treated in ICU or ventilated in the private sector, but decreased odds of black African patients being treated in ICU (aOR 0.5; 95% CI 0.4, 0.5) or ventilated (aOR 0.5; 95% CI 0.4, 0.6) compared to white patients in the public sector. These findings demonstrate the importance of collecting and analysing data on race and socio-economic status to ensure that disease control measures address the most vulnerable populations affected by COVID-19.
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Affiliation(s)
- Waasila Jassat
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Right to Care, Pretoria, South Africa
| | - Lovelyn Ozougwu
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Shehnaz Munshi
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Caroline Mudara
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Caroline Vika
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Tracy Arendse
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Maureen Masha
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Right to Care, Pretoria, South Africa
| | - Richard Welch
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Nevashan Govender
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Joy Ebonwu
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Michelle Groome
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Shabir A. Madhi
- South African Medical Research Council (SAMRC) Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- African Leadership in Vaccinology Expertise (ALIVE), University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Lucille Blumberg
- National Institute for Communicable Diseases (NICD), National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Right to Care, Pretoria, South Africa
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Wulf Hanson S, Abbafati C, Aerts JG, Al-Aly Z, Ashbaugh C, Ballouz T, Blyuss O, Bobkova P, Bonsel G, Borzakova S, Buonsenso D, Butnaru D, Carter A, Chu H, De Rose C, Diab MM, Ekbom E, El Tantawi M, Fomin V, Frithiof R, Gamirova A, Glybochko PV, Haagsma JA, Javanmard SH, Hamilton EB, Harris G, Heijenbrok-Kal MH, Helbok R, Hellemons ME, Hillus D, Huijts SM, Hultström M, Jassat W, Kurth F, Larsson IM, Lipcsey M, Liu C, Loflin CD, Malinovschi A, Mao W, Mazankova L, McCulloch D, Menges D, Mohammadifard N, Munblit D, Nekliudov NA, Ogbuoji O, Osmanov IM, Peñalvo JL, Petersen MS, Puhan MA, Rahman M, Rass V, Reinig N, Ribbers GM, Ricchiuto A, Rubertsson S, Samitova E, Sarrafzadegan N, Shikhaleva A, Simpson KE, Sinatti D, Soriano JB, Spiridonova E, Steinbeis F, Svistunov AA, Valentini P, van de Water BJ, van den Berg-Emons R, Wallin E, Witzenrath M, Wu Y, Xu H, Zoller T, Adolph C, Albright J, Amlag JO, Aravkin AY, Bang-Jensen BL, Bisignano C, Castellano R, Castro E, Chakrabarti S, Collins JK, Dai X, Daoud F, Dapper C, Deen A, Duncan BB, Erickson M, Ewald SB, Ferrari AJ, Flaxman AD, Fullman N, Gamkrelidze A, Giles JR, Guo G, Hay SI, He J, Helak M, Hulland EN, Kereselidze M, Krohn KJ, Lazzar-Atwood A, Lindstrom A, Lozano R, Magistro B, Malta DC, Månsson J, Mantilla Herrera AM, Mokdad AH, Monasta L, Nomura S, Pasovic M, Pigott DM, Reiner RC, Reinke G, Ribeiro ALP, Santomauro DF, Sholokhov A, Spurlock EE, Walcott R, Walker A, Wiysonge CS, Zheng P, Bettger JP, Murray CJ, Vos T. A global systematic analysis of the occurrence, severity, and recovery pattern of long COVID in 2020 and 2021. medRxiv 2022. [PMID: 35664995 PMCID: PMC9164454 DOI: 10.1101/2022.05.26.22275532] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Importance: While much of the attention on the COVID-19 pandemic was directed at the daily counts of cases and those with serious disease overwhelming health services, increasingly, reports have appeared of people who experience debilitating symptoms after the initial infection. This is popularly known as long COVID. Objective: To estimate by country and territory of the number of patients affected by long COVID in 2020 and 2021, the severity of their symptoms and expected pattern of recovery Design: We jointly analyzed ten ongoing cohort studies in ten countries for the occurrence of three major symptom clusters of long COVID among representative COVID cases. The defining symptoms of the three clusters (fatigue, cognitive problems, and shortness of breath) are explicitly mentioned in the WHO clinical case definition. For incidence of long COVID, we adopted the minimum duration after infection of three months from the WHO case definition. We pooled data from the contributing studies, two large medical record databases in the United States, and findings from 44 published studies using a Bayesian meta-regression tool. We separately estimated occurrence and pattern of recovery in patients with milder acute infections and those hospitalized. We estimated the incidence and prevalence of long COVID globally and by country in 2020 and 2021 as well as the severity-weighted prevalence using disability weights from the Global Burden of Disease study. Results: Analyses are based on detailed information for 1906 community infections and 10526 hospitalized patients from the ten collaborating cohorts, three of which included children. We added published data on 37262 community infections and 9540 hospitalized patients as well as ICD-coded medical record data concerning 1.3 million infections. Globally, in 2020 and 2021, 144.7 million (95% uncertainty interval [UI] 54.8–312.9) people suffered from any of the three symptom clusters of long COVID. This corresponds to 3.69% (1.38–7.96) of all infections. The fatigue, respiratory, and cognitive clusters occurred in 51.0% (16.9–92.4), 60.4% (18.9–89.1), and 35.4% (9.4–75.1) of long COVID cases, respectively. Those with milder acute COVID-19 cases had a quicker estimated recovery (median duration 3.99 months [IQR 3.84–4.20]) than those admitted for the acute infection (median duration 8.84 months [IQR 8.10–9.78]). At twelve months, 15.1% (10.3–21.1) continued to experience long COVID symptoms. Conclusions and relevance: The occurrence of debilitating ongoing symptoms of COVID-19 is common. Knowing how many people are affected, and for how long, is important to plan for rehabilitative services and support to return to social activities, places of learning, and the workplace when symptoms start to wane.
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Arendse T, Cowper B, Cohen C, Masha M, Tempia S, Legodu C, Singh S, Ratau T, Geffen L, Heymans A, Coetzer D, Blumberg L, Jassat W. SARS-CoV-2 cases reported from long-term residential facilities (care homes) in South Africa: a retrospective cohort study. BMC Public Health 2022; 22:1035. [PMID: 35606732 PMCID: PMC9126632 DOI: 10.1186/s12889-022-13403-6] [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: 11/16/2021] [Accepted: 05/06/2022] [Indexed: 12/15/2022] Open
Abstract
Background Globally, long-term care facilities (LTCFs) experienced a large burden of deaths during the COVID-19 pandemic. The study aimed to describe the temporal trends as well as the characteristics and risk factors for mortality among residents and staff who tested positive for SARS-CoV-2 in selected LTCFs across South Africa. Method We analysed data reported to the DATCOV sentinel surveillance system by 45 LTCFs. Outbreaks in LTCFs were defined as large if more than one-third of residents and staff had been infected or there were more than 20 epidemiologically linked cases. Multivariable logistic regression was used to assess risk factors for mortality amongst LTCF residents. Results A total of 2324 SARS-CoV-2 cases were reported from 5 March 2020 through 31 July 2021; 1504 (65%) were residents and 820 (35%) staff. Among LTCFs, 6 reported sporadic cases and 39 experienced outbreaks. Of those reporting outbreaks, 10 (26%) reported one and 29 (74%) reported more than one outbreak. There were 48 (66.7%) small outbreaks and 24 (33.3%) large outbreaks reported. There were 30 outbreaks reported in the first wave, 21 in the second wave and 15 in the third wave, with 6 outbreaks reporting between waves. There were 1259 cases during the first COVID-19 wave, 362 during the second wave, and 299 during the current third wave. The case fatality ratio was 9% (138/1504) among residents and 0.5% (4/820) among staff. On multivariable analysis, factors associated with SARS-CoV-2 mortality among LTCF residents were age 40–59 years, 60–79 years and ≥ 80 years compared to < 40 years and being a resident in a LTCF in Free State or Northern Cape compared to Western Cape. Compared to pre-wave 1, there was a decreased risk of mortality in wave 1, post-wave 1, wave 2, post-wave 2 and wave 3. Conclusion The analysis of SARS-CoV-2 cases in sentinel LTCFs in South Africa points to an encouraging trend of decreasing numbers of outbreaks, cases and risk for mortality since the first wave. LTCFs are likely to have learnt from international experience and adopted national protocols, which include improved measures to limit transmission and administer early and appropriate clinical care. Supplementary Information The online version contains supplementary material available at 10.1186/s12889-022-13403-6.
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Affiliation(s)
- Tracy Arendse
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Johannesburg, South Africa. .,Right to Care, Johannesburg, South Africa.
| | | | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Maureen Masha
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Johannesburg, South Africa.,Right to Care, Johannesburg, South Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Civil Legodu
- National Department of Social Development, Pretoria, South Africa
| | - Sandhya Singh
- National Department of Health, Pretoria, South Africa
| | | | - Leon Geffen
- Samson Institute for Ageing Research, Cape Town, South Africa.,Albertina & Walter Sisulu Institute of Ageing in Africa, Geriatrics Unit, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ansie Heymans
- South African Council for Social Workers, Pretoria, South Africa
| | - Dane Coetzer
- South African Nursing Council, Pretoria, South Africa
| | - Lucille Blumberg
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Johannesburg, South Africa.,Right to Care, Johannesburg, South Africa
| | - Waasila Jassat
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Johannesburg, South Africa.,Right to Care, Johannesburg, South Africa
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Bertagnolio S, Thwin SS, Silva R, Nagarajan S, Jassat W, Fowler R, Haniffa R, Reveiz L, Ford N, Doherty M, Diaz J. Clinical features of, and risk factors for, severe or fatal COVID-19 among people living with HIV admitted to hospital: analysis of data from the WHO Global Clinical Platform of COVID-19. Lancet HIV 2022; 9:e486-e495. [PMID: 35561704 PMCID: PMC9090268 DOI: 10.1016/s2352-3018(22)00097-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 01/13/2023]
Abstract
BACKGROUND WHO has established a Global Clinical Platform for the clinical characterisation of COVID-19 among hospitalised individuals. We assessed whether people living with HIV hospitalised with COVID-19 had increased odds of severe presentation and of in-hospital mortality compared with individuals who were HIV-negative and associated risk factors. METHODS Between Jan 1, 2020, and July 1, 2021, anonymised individual-level data from 338 566 patients in 38 countries were reported to WHO. Using the Platform pooled dataset, we performed descriptive statistics and regression analyses to compare outcomes in the two populations and identify risk factors. FINDINGS Of 197 479 patients reporting HIV status, 16 955 (8·6%) were people living with HIV. 16 283 (96.0%) of the 16 955 people living with HIV were from Africa; 10 603 (62·9%) were female and 6271 (37·1%) were male; the mean age was 45·5 years (SD 13·7); 6339 (38·3%) were admitted to hospital with severe illness; and 3913 (24·3%) died in hospital. Of the 10 166 people living with HIV with known antiretroviral therapy (ART) status, 9302 (91·5%) were on ART. Compared with individuals without HIV, people living with HIV had 15% increased odds of severe presentation with COVID-19 (aOR 1·15, 95% CI 1·10-1·20) and were 38% more likely to die in hospital (aHR 1·38, 1·34-1·41). Among people living with HIV, male sex, age 45-75 years, and having chronic cardiac disease or hypertension increased the odds of severe COVID-19; male sex, age older than 18 years, having diabetes, hypertension, malignancy, tuberculosis, or chronic kidney disease increased the risk of in-hospital mortality. The use of ART or viral load suppression were associated with a reduced risk of poor outcomes; however, HIV infection remained a risk factor for severity and mortality regardless of ART and viral load suppression status. INTERPRETATION In this sample of hospitalised people contributing data to the WHO Global Clinical Platform for COVID-19, HIV was an independent risk factor for both severe COVID-19 at admission and in-hospital mortality. These findings have informed WHO immunisation policy that prioritises vaccination for people living with HIV. As the results mostly reflect the data contribution from Africa, this analysis will be updated as more data from other regions become available. FUNDING None. TRANSLATION For the French translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Silvia Bertagnolio
- Department of Global HIV, STI & Hepatitis Programmes, WHO, Geneva, Switzerland,Correspondence to: Dr Silvia Bertagnolio, Department of Global HIV, STI & Hepatitis Programmes, WHO, Geneva 1211, Switzerland
| | - Soe Soe Thwin
- Department of Sexual and Reproductive Health and Research, WHO, Geneva, Switzerland
| | - Ronaldo Silva
- Department of Sexual and Reproductive Health and Research, WHO, Geneva, Switzerland
| | - Sairaman Nagarajan
- Departments of Internal Medicine and Pediatrics, SUNY Downstate Medical Center, New York, USA
| | - Waasila Jassat
- National Institute for Communicable Diseases, Johannesburg, South Africa,Right to Care, Pretoria, South Africa
| | - Robert Fowler
- Department of Medicine, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Rashan Haniffa
- Mahidol Oxford Tropical Medicine Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK,National Intensive Care Surveillance-MORU, Colombo, Sri Lanka
| | - Ludovic Reveiz
- Department of Evidence and Intelligence for Action in Health, Incident Management Systems, Pan American Health Organization, Washington DC, USA
| | - Nathan Ford
- Department of Global HIV, STI & Hepatitis Programmes, WHO, Geneva, Switzerland
| | - Meg Doherty
- Department of Global HIV, STI & Hepatitis Programmes, WHO, Geneva, Switzerland
| | - Janet Diaz
- Department of Country Readiness Strengthening, Health Emergencies Programme, WHO, Geneva, Switzerland
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Ratshikhopha E, Muvhali M, Naicker N, Tlotleng N, Jassat W, Singh T. Disease Severity and Comorbidities among Healthcare Worker COVID-19 Admissions in South Africa: A Retrospective Analysis. Int J Environ Res Public Health 2022; 19:ijerph19095519. [PMID: 35564914 PMCID: PMC9104097 DOI: 10.3390/ijerph19095519] [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] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/22/2022] [Accepted: 04/24/2022] [Indexed: 01/08/2023]
Abstract
Healthcare workers (HCWs) are among the most vulnerable in regard to contracting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Comorbidities are reported to increase the risk for more severe COVID-19 outcomes, often requiring hospitalization. However, the evidence on disease severity and comorbidities among South African HCWs is lacking. This retrospective study analyzed the prevalence of comorbidities among HCW hospitalized with COVID-19 and its association with the severity of outcomes. Data from public and private hospitals in nine provinces of South Africa were extracted from the national hospital surveillance database for COVID-19 admissions. A total of 10,149 COVID-19 HCWs admissions were reported from 5 March 2020 to 31 December 2021. The risk of disease severity among HCWs increased with age, with those older (≥60 years) having seven times the odds of disease severity (aOR 7.0; 95% CI 4.2–11.8) compared to HCWs in the younger age (20–29 years) group. The most commonly reported comorbidity was hypertension (36.3%), followed by diabetes (23.3%) and obesity (16.7%). Hypertension (aOR 1.3; 95% CI 1.0–1.6), diabetes (aOR 1.6; 95% CI 1.3–2.0), and HIV (aOR 1.6; 95% CI 1.2–2.1) were significantly associated with disease severity. In conclusion, age, gender, and existing comorbidities were strong predictors of the prognosis of severe COVID-19 among HCWs in South Africa. The information is important in the development of occupational health policies and vulnerability risk assessments for HCWs in light of future COVID-19 waves or similar outbreaks.
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Affiliation(s)
- Edith Ratshikhopha
- National Health Laboratory Service, National Institute for Occupational Health, Johannesburg 2000, South Africa; (E.R.); (M.M.); (N.T.)
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Munyadziwa Muvhali
- National Health Laboratory Service, National Institute for Occupational Health, Johannesburg 2000, South Africa; (E.R.); (M.M.); (N.T.)
| | - Nisha Naicker
- Department of Environmental Health, University of Johannesburg, Doornfontein 2028, South Africa;
| | - Nonhlanhla Tlotleng
- National Health Laboratory Service, National Institute for Occupational Health, Johannesburg 2000, South Africa; (E.R.); (M.M.); (N.T.)
| | - Waasila Jassat
- National Health Laboratory Service, National Institute for Communicable Diseases, Sandringham 2192, South Africa;
| | - Tanusha Singh
- National Health Laboratory Service, National Institute for Occupational Health, Johannesburg 2000, South Africa; (E.R.); (M.M.); (N.T.)
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, University of the Witwatersrand, Johannesburg 2000, South Africa
- Department of Environmental Health, University of Johannesburg, Doornfontein 2028, South Africa;
- Correspondence:
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Jassat W, Abdool Karim SS, Mudara C, Welch R, Ozougwu L, Groome MJ, Govender N, von Gottberg A, Wolter N, Wolmarans M, Rousseau P, Blumberg L, Cohen C. Clinical severity of COVID-19 in patients admitted to hospital during the omicron wave in South Africa: a retrospective observational study. The Lancet Global Health 2022; 10:e961-e969. [PMID: 35597249 PMCID: PMC9116895 DOI: 10.1016/s2214-109x(22)00114-0] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
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Kleynhans J, Tempia S, Wolter N, von Gottberg A, Bhiman JN, Buys A, Moyes J, McMorrow ML, Kahn K, Gómez-Olivé FX, Tollman S, Martinson NA, Wafawanaka F, Lebina L, du Toit JD, Jassat W, Neti M, Brauer M, Cohen C. SARS-CoV-2 Seroprevalence after Third Wave of Infections, South Africa. Emerg Infect Dis 2022; 28:1055-1058. [PMID: 35320701 PMCID: PMC9045427 DOI: 10.3201/eid2805.220278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
By November 2021, after the third wave of severe acute respiratory syndrome coronavirus 2 infections in South Africa, seroprevalence was 60% in a rural community and 70% in an urban community. High seroprevalence before the Omicron variant emerged may have contributed to reduced illness severity observed in the fourth wave.
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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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Affiliation(s)
- Alex Sigal
- Africa Health Research Institute, Durban, South Africa.
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
- Max Planck Institute for Infection Biology, Berlin, Germany.
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa.
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Waasila Jassat
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Right to Care, Centurion, South Africa
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Madhi SA, Kwatra G, Myers JE, Jassat W, Dhar N, Mukendi CK, Nana AJ, Blumberg L, Welch R, Ngorima-Mabhena N, Mutevedzi PC. Population Immunity and Covid-19 Severity with Omicron Variant in South Africa. N Engl J Med 2022; 386:1314-1326. [PMID: 35196424 PMCID: PMC8908853 DOI: 10.1056/nejmoa2119658] [Citation(s) in RCA: 221] [Impact Index Per Article: 110.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND The B.1.1.529 (omicron) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified on November 25, 2021, in Gauteng province, South Africa. Data regarding the seroprevalence of SARS-CoV-2 IgG in Gauteng before the fourth wave of coronavirus disease 2019 (Covid-19), in which the omicron variant was dominant, are needed. METHODS We conducted a seroepidemiologic survey from October 22 to December 9, 2021, in Gauteng to determine the seroprevalence of SARS-CoV-2 IgG. Households included in a previous seroepidemiologic survey (conducted from November 2020 to January 2021) were contacted; to account for changes in the survey population, there was a 10% increase in the households contacted, with the use of the same sampling framework. Dried-blood-spot samples were tested for IgG against SARS-CoV-2 spike protein and nucleocapsid protein with the use of quantitative assays. We also evaluated Covid-19 epidemiologic trends in Gauteng, including cases, hospitalizations, recorded deaths, and excess deaths from the start of the pandemic through January 12, 2022. RESULTS Samples were obtained from 7010 participants, of whom 1319 (18.8%) had received a Covid-19 vaccine. The seroprevalence of SARS-CoV-2 IgG ranged from 56.2% (95% confidence interval [CI], 52.6 to 59.7) among children younger than 12 years of age to 79.7% (95% CI, 77.6 to 81.5) among adults older than 50 years of age. Vaccinated participants were more likely to be seropositive for SARS-CoV-2 than unvaccinated participants (93.1% vs. 68.4%). Epidemiologic data showed that the incidence of SARS-CoV-2 infection increased and subsequently declined more rapidly during the fourth wave than it had during the three previous waves. The incidence of infection was decoupled from the incidences of hospitalization, recorded death, and excess death during the fourth wave, as compared with the proportions seen during previous waves. CONCLUSIONS Widespread underlying SARS-CoV-2 seropositivity was observed in Gauteng before the omicron-dominant wave of Covid-19. Epidemiologic data showed a decoupling of hospitalizations and deaths from infections while omicron was circulating. (Funded by the Bill and Melinda Gates Foundation.).
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Affiliation(s)
- Shabir A Madhi
- From the South African Medical Research Council Vaccine and Infectious Diseases Analytics Research Unit (S.A.M., G.K., N.D., C.K.M., A.J.N., P.C.M.) and African Leadership in Vaccinology Expertise (S.A.M., G.K.), University of the Witwatersrand, the National Institute for Communicable Diseases, National Health Laboratory Service (W.J., L.B., R.W.), and ResearchLinkMe (N.N.-M.), Johannesburg, the Centre for Environmental and Occupational Health Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town (J.E.M.), and Right to Care, Centurion (L.B.) - all in South Africa
| | - Gaurav Kwatra
- From the South African Medical Research Council Vaccine and Infectious Diseases Analytics Research Unit (S.A.M., G.K., N.D., C.K.M., A.J.N., P.C.M.) and African Leadership in Vaccinology Expertise (S.A.M., G.K.), University of the Witwatersrand, the National Institute for Communicable Diseases, National Health Laboratory Service (W.J., L.B., R.W.), and ResearchLinkMe (N.N.-M.), Johannesburg, the Centre for Environmental and Occupational Health Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town (J.E.M.), and Right to Care, Centurion (L.B.) - all in South Africa
| | - Jonathan E Myers
- From the South African Medical Research Council Vaccine and Infectious Diseases Analytics Research Unit (S.A.M., G.K., N.D., C.K.M., A.J.N., P.C.M.) and African Leadership in Vaccinology Expertise (S.A.M., G.K.), University of the Witwatersrand, the National Institute for Communicable Diseases, National Health Laboratory Service (W.J., L.B., R.W.), and ResearchLinkMe (N.N.-M.), Johannesburg, the Centre for Environmental and Occupational Health Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town (J.E.M.), and Right to Care, Centurion (L.B.) - all in South Africa
| | - Waasila Jassat
- From the South African Medical Research Council Vaccine and Infectious Diseases Analytics Research Unit (S.A.M., G.K., N.D., C.K.M., A.J.N., P.C.M.) and African Leadership in Vaccinology Expertise (S.A.M., G.K.), University of the Witwatersrand, the National Institute for Communicable Diseases, National Health Laboratory Service (W.J., L.B., R.W.), and ResearchLinkMe (N.N.-M.), Johannesburg, the Centre for Environmental and Occupational Health Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town (J.E.M.), and Right to Care, Centurion (L.B.) - all in South Africa
| | - Nisha Dhar
- From the South African Medical Research Council Vaccine and Infectious Diseases Analytics Research Unit (S.A.M., G.K., N.D., C.K.M., A.J.N., P.C.M.) and African Leadership in Vaccinology Expertise (S.A.M., G.K.), University of the Witwatersrand, the National Institute for Communicable Diseases, National Health Laboratory Service (W.J., L.B., R.W.), and ResearchLinkMe (N.N.-M.), Johannesburg, the Centre for Environmental and Occupational Health Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town (J.E.M.), and Right to Care, Centurion (L.B.) - all in South Africa
| | - Christian K Mukendi
- From the South African Medical Research Council Vaccine and Infectious Diseases Analytics Research Unit (S.A.M., G.K., N.D., C.K.M., A.J.N., P.C.M.) and African Leadership in Vaccinology Expertise (S.A.M., G.K.), University of the Witwatersrand, the National Institute for Communicable Diseases, National Health Laboratory Service (W.J., L.B., R.W.), and ResearchLinkMe (N.N.-M.), Johannesburg, the Centre for Environmental and Occupational Health Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town (J.E.M.), and Right to Care, Centurion (L.B.) - all in South Africa
| | - Amit J Nana
- From the South African Medical Research Council Vaccine and Infectious Diseases Analytics Research Unit (S.A.M., G.K., N.D., C.K.M., A.J.N., P.C.M.) and African Leadership in Vaccinology Expertise (S.A.M., G.K.), University of the Witwatersrand, the National Institute for Communicable Diseases, National Health Laboratory Service (W.J., L.B., R.W.), and ResearchLinkMe (N.N.-M.), Johannesburg, the Centre for Environmental and Occupational Health Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town (J.E.M.), and Right to Care, Centurion (L.B.) - all in South Africa
| | - Lucille Blumberg
- From the South African Medical Research Council Vaccine and Infectious Diseases Analytics Research Unit (S.A.M., G.K., N.D., C.K.M., A.J.N., P.C.M.) and African Leadership in Vaccinology Expertise (S.A.M., G.K.), University of the Witwatersrand, the National Institute for Communicable Diseases, National Health Laboratory Service (W.J., L.B., R.W.), and ResearchLinkMe (N.N.-M.), Johannesburg, the Centre for Environmental and Occupational Health Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town (J.E.M.), and Right to Care, Centurion (L.B.) - all in South Africa
| | - Richard Welch
- From the South African Medical Research Council Vaccine and Infectious Diseases Analytics Research Unit (S.A.M., G.K., N.D., C.K.M., A.J.N., P.C.M.) and African Leadership in Vaccinology Expertise (S.A.M., G.K.), University of the Witwatersrand, the National Institute for Communicable Diseases, National Health Laboratory Service (W.J., L.B., R.W.), and ResearchLinkMe (N.N.-M.), Johannesburg, the Centre for Environmental and Occupational Health Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town (J.E.M.), and Right to Care, Centurion (L.B.) - all in South Africa
| | - Nicoletta Ngorima-Mabhena
- From the South African Medical Research Council Vaccine and Infectious Diseases Analytics Research Unit (S.A.M., G.K., N.D., C.K.M., A.J.N., P.C.M.) and African Leadership in Vaccinology Expertise (S.A.M., G.K.), University of the Witwatersrand, the National Institute for Communicable Diseases, National Health Laboratory Service (W.J., L.B., R.W.), and ResearchLinkMe (N.N.-M.), Johannesburg, the Centre for Environmental and Occupational Health Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town (J.E.M.), and Right to Care, Centurion (L.B.) - all in South Africa
| | - Portia C Mutevedzi
- From the South African Medical Research Council Vaccine and Infectious Diseases Analytics Research Unit (S.A.M., G.K., N.D., C.K.M., A.J.N., P.C.M.) and African Leadership in Vaccinology Expertise (S.A.M., G.K.), University of the Witwatersrand, the National Institute for Communicable Diseases, National Health Laboratory Service (W.J., L.B., R.W.), and ResearchLinkMe (N.N.-M.), Johannesburg, the Centre for Environmental and Occupational Health Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town (J.E.M.), and Right to Care, Centurion (L.B.) - all in South Africa
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Bekker LG, Garrett N, Goga A, Fairall L, Reddy T, Yende-Zuma N, Kassanjee R, Collie S, Sanne I, Boulle A, Seocharan I, Engelbrecht I, Davies MA, Champion J, Chen T, Bennett S, Mametja S, Semenya M, Moultrie H, de Oliveira T, Lessells RJ, Cohen C, Jassat W, Groome M, Von Gottberg A, Le Roux E, Khuto K, Barouch D, Mahomed H, Wolmarans M, Rousseau P, Bradshaw D, Mulder M, Opie J, Louw V, Jacobson B, Rowji P, Peter JG, Takalani A, Odhiambo J, Mayat F, Takuva S, Corey L, Gray GE. Effectiveness of the Ad26.COV2.S vaccine in health-care workers in South Africa (the Sisonke study): results from a single-arm, open-label, phase 3B, implementation study. Lancet 2022; 399:1141-1153. [PMID: 35305740 PMCID: PMC8930006 DOI: 10.1016/s0140-6736(22)00007-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/18/2021] [Accepted: 12/13/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND We aimed to assess the effectiveness of a single dose of the Ad26.COV2.S vaccine (Johnson & Johnson) in health-care workers in South Africa during two waves of the South African COVID-19 epidemic. METHODS In the single-arm, open-label, phase 3B implementation Sisonke study, health-care workers aged 18 years and older were invited for vaccination at one of 122 vaccination sites nationally. Participants received a single dose of 5 × 1010 viral particles of the Ad26.COV2.S vaccine. Vaccinated participants were linked with their person-level data from one of two national medical insurance schemes (scheme A and scheme B) and matched for COVID-19 risk with an unvaccinated member of the general population. The primary outcome was vaccine effectiveness against severe COVID-19, defined as COVID-19-related admission to hospital, hospitalisation requiring critical or intensive care, or death, in health-care workers compared with the general population, ascertained 28 days or more after vaccination or matching, up to data cutoff. This study is registered with the South African National Clinical Trial Registry, DOH-27-022021-6844, ClinicalTrials.gov, NCT04838795, and the Pan African Clinical Trials Registry, PACTR202102855526180, and is closed to accrual. FINDINGS Between Feb 17 and May 17, 2021, 477 102 health-care workers were enrolled and vaccinated, of whom 357 401 (74·9%) were female and 119 701 (25·1%) were male, with a median age of 42·0 years (33·0-51·0). 215 813 vaccinated individuals were matched with 215 813 unvaccinated individuals. As of data cutoff (July 17, 2021), vaccine effectiveness derived from the total matched cohort was 83% (95% CI 75-89) to prevent COVID-19-related deaths, 75% (69-82) to prevent COVID-19-related hospital admissions requiring critical or intensive care, and 67% (62-71) to prevent COVID-19-related hospitalisations. The vaccine effectiveness for all three outcomes were consistent across scheme A and scheme B. The vaccine effectiveness was maintained in older health-care workers and those with comorbidities including HIV infection. During the course of the study, the beta (B.1.351) and then the delta (B.1.617.2) SARS-CoV-2 variants of concerns were dominant, and vaccine effectiveness remained consistent (for scheme A plus B vaccine effectiveness against COVID-19-related hospital admission during beta wave was 62% [95% CI 42-76] and during delta wave was 67% [62-71], and vaccine effectiveness against COVID-19-related death during beta wave was 86% [57-100] and during delta wave was 82% [74-89]). INTERPRETATION The single-dose Ad26.COV2.S vaccine shows effectiveness against severe COVID-19 disease and COVID-19-related death after vaccination, and against both beta and delta variants, providing real-world evidence for its use globally. FUNDING National Treasury of South Africa, the National Department of Health, Solidarity Response Fund NPC, The Michael & Susan Dell Foundation, The Elma Vaccines and Immunization Foundation, and the Bill & Melinda Gates Foundation.
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Affiliation(s)
- Linda-Gail Bekker
- The Desmond Tutu HIV Centre, Cape Town, South Africa; University of Cape Town, Cape Town, South Africa
| | - Nigel Garrett
- Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Ameena Goga
- HIV Prevention Research Unit, Cape Town, South Africa; Department of Paediatrics and Child Health, University of Pretoria, Pretoria, South Africa
| | - Lara Fairall
- The Desmond Tutu HIV Centre, Cape Town, South Africa; King's Global Health Institute, King's College London, London, UK
| | - Tarylee Reddy
- Biostatistics Research Unit, South African Medical Research Council, Durban, South Africa
| | - Nonhlanhla Yende-Zuma
- Nelson R Mandela School of Medicine, Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Reshma Kassanjee
- Centre of Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, Cape Town, South Africa
| | | | - Ian Sanne
- Clinical HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Witwatersrand, South Africa; Right to Care, Houghton South Africa
| | - Andrew Boulle
- Centre of Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, Cape Town, South Africa; Western Cape Government Health, Cape Town, South Africa; Wellcome Centre for Infectious Diseases Research in Africa, Cape Town, South Africa
| | - Ishen Seocharan
- Biostatistics Research Unit, South African Medical Research Council, Durban, South Africa
| | | | - Mary-Ann Davies
- Centre of Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, Cape Town, South Africa; Western Cape Government: Health Centre for Infectious Disease Epidemiology and Research, Cape Town, South Africa
| | | | | | | | | | | | - Harry Moultrie
- Centre for Tuberculosis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Richard John Lessells
- KwaZulu-Natal Research Innovation, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Cheryl Cohen
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Witwatersrand, South Africa; Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Waasila Jassat
- National Institute for Communicable Diseases, Sandringham, South Africa
| | - Michelle Groome
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Witwatersrand, South Africa; Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Anne Von Gottberg
- Department of Pathology, Cape Town, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Witwatersrand, South Africa; Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Engelbert Le Roux
- Hutchinson Center Research Institute of South Africa (HCRISA), Chris Hani Baragwanath Academic Hospital, Soweto, South Africa
| | - Kentse Khuto
- Hutchinson Center Research Institute of South Africa (HCRISA), Chris Hani Baragwanath Academic Hospital, Soweto, South Africa
| | - Dan Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - 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, Cape Town, South Africa
| | | | | | - Debbie Bradshaw
- South African Medical Research Council, Tygerberg, South Africa
| | - Michelle Mulder
- South Africa Medical Research Council, Cape Town, South Africa
| | - Jessica Opie
- University of Cape Town, Cape Town, South Africa; National Health Laboratory Service, Cape Town, South Africa
| | - Vernon Louw
- Division of Clinical Haematology, Department of Medicine, Cape Town, South Africa; Groote Schuur Hospital, Cape Town, South Africa
| | - Barry Jacobson
- Faculty of Health Sciences, and Allergy and Immunology Unit, Cape Town, South Africa
| | - Pradeep Rowji
- Neurology Association of South Africa, The Southern African Society of Thrombosis and Haemostasis, Johannesburg, South Africa
| | - Jonny G Peter
- Division of Allergy and Clinical Immunology, Cape Town, South Africa
| | - Azwi Takalani
- Hutchinson Center Research Institute of South Africa (HCRISA), Chris Hani Baragwanath Academic Hospital, Soweto, South Africa
| | - Jackline Odhiambo
- Hutchinson Center Research Institute of South Africa (HCRISA), Chris Hani Baragwanath Academic Hospital, Soweto, South Africa
| | - Fatima Mayat
- Perinatal HIV Research Unit (PHRU), Chris Hani Baragwanath Academic Hospital, University of the Witwatersrand, Witwatersrand, South Africa
| | - Simbarashe Takuva
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Glenda E Gray
- South Africa Medical Research Council, Cape Town, South Africa.
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Cloete J, Kruger A, Masha M, du Plessis NM, Mawela D, Tshukudu M, Manyane T, Komane L, Venter M, Jassat W, Goga A, Feucht U. Paediatric hospitalisations due to COVID-19 during the first SARS-CoV-2 omicron (B.1.1.529) variant wave in South Africa: a multicentre observational study. Lancet Child Adolesc Health 2022; 6:294-302. [PMID: 35189083 PMCID: PMC8856663 DOI: 10.1016/s2352-4642(22)00027-x] [Citation(s) in RCA: 106] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 12/13/2022]
Abstract
Background South Africa reported a notable increase in COVID-19 cases from mid-November, 2021, onwards, starting in Tshwane District, which coincided with the rapid community spread of the SARS-CoV-2 omicron (B.1.1.529) variant. This increased infection rate coincided with a rapid increase in paediatric COVID-19-associated admissions to hospital (hereafter referred to as hospitalisations). Methods The Tshwane Maternal-Child COVID-19 study is a multicentre observational study in which we investigated the clinical manifestations and outcomes of paediatric patients (aged ≤19 years) who had tested positive for SARS-CoV-2 and were admitted to hospital for any reason in Tshwane District during a 6-week period at the beginning of the fourth wave of the COVID-19 epidemic in South Africa. We used five data sources, which were: (1) COVID-19 line lists; (2) collated SARS-CoV-2 testing data; (3) SARS-CoV-2 genomic sequencing data; (4) COVID-19 hospitalisation surveillance; and (5) clinical data of public sector COVID-19-associated hospitalisations among children aged 13 years and younger. Findings Between Oct 31 and Dec 11, 2021, 6287 children and adolescents in Tshwane District were recorded as having COVID-19. During this period, 2550 people with COVID-19 were hospitalised, of whom 462 (18%) were aged 19 years or younger. The number of paediatric cases was higher than in the three previous SARS-CoV-2 waves, uncharacteristically increasing ahead of adult hospitalisations. 75 viral samples from adults and children in the district were sequenced, of which 74 (99%) were of the omicron variant. Detailed clinical notes were available for 138 (75%) of 183 children aged ≤13 years with COVID-19 who were hospitalised. 87 (63%) of 138 children were aged 0–4 years. In 61 (44%) of 138 cases COVID-19 was the primary diagnosis, among whom symptoms included fever (37 [61%] of 61), cough (35 [57%]), shortness of breath (19 [31%]), seizures (19 [31%]), vomiting (16 [26%]), and diarrhoea (15 [25%]). Median length of hospital stay was 2 days [IQR 1–3]). 122 (88%) of 138 children with available data needed standard ward care and 27 (20%) needed oxygen therapy. Seven (5%) of 138 children were ventilated and four (3%) died during the study period, all related to complex underlying copathologies. All children and 77 (92%) of 84 parents or guardians with available data were unvaccinated to COVID-19. Interpretation Rapid increases in paediatric COVID-19 cases and hospitalisations mirror high community transmission of the SARS-CoV-2 omicron variant in Tshwane District, South Africa. Continued monitoring is needed to understand the long-term effect of the omicron variant on children and adolescents. Funding South African Medical Research Council, South African Department of Science & Innovation, G7 Global Health Fund.
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Affiliation(s)
- Jeané Cloete
- Department of Paediatrics and Child Health, University of Pretoria, Pretoria, South Africa; Centre for Maternal, Fetal, Newborn and Child Health Care Strategies, University of Pretoria, Pretoria, South Africa; Maternal and Infant Health Care Strategies Research Unit, South African Medical Research Council, Pretoria, South Africa.
| | - Annelet Kruger
- Centre for Maternal, Fetal, Newborn and Child Health Care Strategies, University of Pretoria, Pretoria, South Africa; Department of Family Medicine, University of Pretoria, Pretoria, South Africa; Maternal and Infant Health Care Strategies Research Unit, South African Medical Research Council, Pretoria, South Africa; Tshwane District Health Services, Gauteng Department of Health, Pretoria, South Africa
| | - Maureen Masha
- National Institute of Communicable Diseases, Johannesburg, South Africa; Right to Care, Johannesburg, South Africa
| | - Nicolette M du Plessis
- Department of Paediatrics and Child Health, University of Pretoria, Pretoria, South Africa; Centre for Maternal, Fetal, Newborn and Child Health Care Strategies, University of Pretoria, Pretoria, South Africa; Maternal and Infant Health Care Strategies Research Unit, South African Medical Research Council, Pretoria, South Africa
| | - Dini Mawela
- Department of Paediatrics, Sefako Makgatho Health Sciences University, Dr George Mukhari Academic Hospital, Pretoria, South Africa
| | - Mphailele Tshukudu
- Tshwane District Health Services, Gauteng Department of Health, Pretoria, South Africa
| | - Tabea Manyane
- Tshwane District Health Services, Gauteng Department of Health, Pretoria, South Africa
| | - Lekwetji Komane
- Tshwane District Health Services, Gauteng Department of Health, Pretoria, South Africa
| | - Marietjie Venter
- Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Waasila Jassat
- National Institute of Communicable Diseases, Johannesburg, South Africa
| | - Ameena Goga
- Department of Paediatrics and Child Health, University of Pretoria, Pretoria, South Africa; HIV Prevention Research Unit, South African Medical Research Council, Pretoria, South Africa
| | - Ute Feucht
- Department of Paediatrics and Child Health, University of Pretoria, Pretoria, South Africa; Centre for Maternal, Fetal, Newborn and Child Health Care Strategies, University of Pretoria, Pretoria, South Africa; Maternal and Infant Health Care Strategies Research Unit, South African Medical Research Council, Pretoria, South Africa; Tshwane District Health Services, Gauteng Department of Health, Pretoria, South Africa
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Ovens W, Tomescu S, Harrison E, Crampton T, De Nooy A, Jassat W, Banoo S, Pisa P, Sanne I. Guiding equitable prioritisation of COVID-19 vaccine distribution and strategic deployment in South Africa to enhance effectiveness and access to vulnerable communities and prevent waste. S Afr Med J 2022; 112:13501. [PMID: 35139989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND In South Africa (SA), >2.4 million cases of COVID‑19 and >72 000 deaths were recorded between March 2020 and 1 August 2021, affecting the country's 52 districts to various extents. SA has committed to a COVID‑19 vaccine roll-out in three phases, prioritising frontline workers, the elderly, people with comorbidities and essential workers. However, additional actions will be necessary to support efficient allocation and equitable access for vulnerable, access-constrained communities. OBJECTIVES To explore various determinants of disease severity, resurgence risk and accessibility in order to aid an equitable, effective vaccine roll-out for SA that would maximise COVID‑19 epidemic control by reducing the number of COVID‑19 transmissions and resultant deaths, while at the same time reducing the risk of vaccine wastage. METHODS For the 52 districts of SA, 26 COVID‑19 indicators such as hospital admissions, deaths in hospital and mobility were ranked and hierarchically clustered with cases to identify which indicators can be used as indicators for severity or resurgence risk. Districts were then ranked using the estimated COVID‑19 severity and resurgence risk to assist with prioritisation of vaccine roll-out. Urban and rural accessibility were also explored as factors that could limit vaccine roll-out in hard-to-reach communities. RESULTS Highly populated urban districts showed the most cases. Districts such as Buffalo City, City of Cape Town and Nelson Mandela Bay experienced very severe first and second waves of the pandemic. Districts with high mobility, population size and density were found to be at highest risk of resurgence. In terms of accessibility, we found that 47.2% of the population are within 5 km of a hospital with ≥50 beds, and this percentage ranged from 87.0% in City of Cape Town to 0% in Namakwa district. CONCLUSIONS The end goal is to provide equal distribution of vaccines proportional to district populations, which will provide fair protection. Districts with a high risk of resurgence and severity should be prioritised for vaccine roll-out, particularly the major metropolitan areas. We provide recommendations for allocations of different vaccine types for each district that consider levels of access, numbers of doses and cold-chain storage capability.
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Affiliation(s)
- W Ovens
- Right to Care, Centurion, Pretoria, South Africa.
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48
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Wolter N, Jassat W, Walaza S, Welch R, Moultrie H, Groome M, Amoako DG, Everatt J, Bhiman JN, Scheepers C, Tebeila N, Chiwandire N, du Plessis M, Govender N, Ismail A, Glass A, Mlisana K, Stevens W, Treurnicht FK, Makatini Z, Hsiao NY, Parboosing R, Wadula J, Hussey H, Davies MA, Boulle A, von Gottberg A, Cohen C. Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study. Lancet 2022; 399:437-446. [PMID: 35065011 PMCID: PMC8769664 DOI: 10.1016/s0140-6736(22)00017-4] [Citation(s) in RCA: 613] [Impact Index Per Article: 306.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 12/24/2021] [Accepted: 01/04/2022] [Indexed: 12/20/2022]
Abstract
BACKGROUND The SARS-CoV-2 omicron variant of concern was identified in South Africa in November, 2021, and was associated with an increase in COVID-19 cases. We aimed to assess the clinical severity of infections with the omicron variant using S gene target failure (SGTF) on the Thermo Fisher Scientific TaqPath COVID-19 PCR test as a proxy. METHODS We did data linkages for national, South African COVID-19 case data, SARS-CoV-2 laboratory test data, SARS-CoV-2 genome data, and COVID-19 hospital admissions data. For individuals diagnosed with COVID-19 via TaqPath PCR tests, infections were designated as either SGTF or non-SGTF. The delta variant was identified by genome sequencing. Using multivariable logistic regression models, we assessed disease severity and hospitalisations by comparing individuals with SGTF versus non-SGTF infections diagnosed between Oct 1 and Nov 30, 2021, and we further assessed disease severity by comparing SGTF-infected individuals diagnosed between Oct 1 and Nov 30, 2021, with delta variant-infected individuals diagnosed between April 1 and Nov 9, 2021. FINDINGS From Oct 1 (week 39), 2021, to Dec 6 (week 49), 2021, 161 328 cases of COVID-19 were reported in South Africa. 38 282 people were diagnosed via TaqPath PCR tests and 29 721 SGTF infections and 1412 non-SGTF infections were identified. The proportion of SGTF infections increased from two (3·2%) of 63 in week 39 to 21 978 (97·9%) of 22 455 in week 48. After controlling for factors associated with hospitalisation, individuals with SGTF infections had significantly lower odds of admission than did those with non-SGTF infections (256 [2·4%] of 10 547 vs 121 [12·8%] of 948; adjusted odds ratio [aOR] 0·2, 95% CI 0·1-0·3). After controlling for factors associated with disease severity, the odds of severe disease were similar between hospitalised individuals with SGTF versus non-SGTF infections (42 [21%] of 204 vs 45 [40%] of 113; aOR 0·7, 95% CI 0·3-1·4). Compared with individuals with earlier delta variant infections, SGTF-infected individuals had a significantly lower odds of severe disease (496 [62·5%] of 793 vs 57 [23·4%] of 244; aOR 0·3, 95% CI 0·2-0·5), after controlling for factors associated with disease severity. INTERPRETATION Our early analyses suggest a significantly reduced odds of hospitalisation among individuals with SGTF versus non-SGTF infections diagnosed during the same time period. SGTF-infected individuals had a significantly reduced odds of severe disease compared with individuals infected earlier with the delta variant. Some of this reduced severity is probably a result of previous immunity. FUNDING The South African Medical Research Council, the South African National Department of Health, US Centers for Disease Control and Prevention, the African Society of Laboratory Medicine, Africa Centers for Disease Control and Prevention, the Bill & Melinda Gates Foundation, the Wellcome Trust, and the Fleming Fund.
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Affiliation(s)
- Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Waasila Jassat
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, 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 Welch
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Harry Moultrie
- Centre for Tuberculosis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michelle Groome
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Daniel Gyamfi Amoako
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Josie Everatt
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Jinal N Bhiman
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cathrine Scheepers
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Naume Tebeila
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nicola Chiwandire
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nevashan Govender
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | | | - Koleka Mlisana
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; National Health Laboratory Service, Johannesburg, South Africa
| | - Wendy Stevens
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; National Health Laboratory Service, Johannesburg, South Africa
| | - Florette K Treurnicht
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; National Health Laboratory Service, Johannesburg, South Africa
| | - Zinhle Makatini
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; National Health Laboratory Service, Johannesburg, South Africa
| | - Nei-Yuan Hsiao
- National Health Laboratory Service, Johannesburg, South Africa; Division of Medical Virology, University of Cape Town, Cape Town, South Africa
| | - Raveen Parboosing
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Virology, University of KwaZulu-Natal, Durban, South Africa; National Health Laboratory Service, Johannesburg, South Africa
| | - Jeannette Wadula
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; National Health Laboratory Service, Johannesburg, South Africa; Department of Clinical Microbiology and Infectious Diseases, CH Baragwanath Academic Hospital, Johannesburg, South Africa
| | - Hannah Hussey
- Western Cape Government Health and School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Mary-Ann Davies
- Western Cape Government Health and School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Andrew Boulle
- Western Cape Government Health and School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, 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.
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49
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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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50
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Abdullah F, Myers J, Basu D, Tintinger G, Ueckermann V, Mathebula M, Ramlall R, Spoor S, de Villiers T, Van der Walt Z, Cloete J, Soma-Pillay P, Rheeder P, Paruk F, Engelbrecht A, Lalloo V, Myburg M, Kistan J, van Hougenhouck-Tulleken W, Boswell MT, Gray G, Welch R, Blumberg L, Jassat W. Decreased severity of disease during the first global omicron variant covid-19 outbreak in a large hospital in tshwane, south africa. Int J Infect Dis 2021; 116:38-42. [PMID: 34971823 PMCID: PMC8713416 DOI: 10.1016/j.ijid.2021.12.357] [Citation(s) in RCA: 239] [Impact Index Per Article: 79.7] [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: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION The coronavirus disease 2019 (COVID-19) first reported in Wuhan China in December 2019 is a global pandemic that is threatening the health and wellbeing of people worldwide. To date there have been more than 274 million reported cases and 5.3 million deaths. The Omicron variant first documented in the City of Tshwane, Gauteng Province, South Africa on 9 November 2021 led to exponential increases in cases and a sharp rise in hospital admissions. The clinical profile of patients admitted at a large hospital in Tshwane is compared with previous waves. METHODS The methods should describe what study design you employed for the study and what your sample size was, as it is this is mainly results. 466 hospital COVID-19 admissions since 14 November 2021 were compared to 3976 prior admissions since 4 May 2020. Ninety-eight patient records at peak bed occupancy during the outbreak were reviewed for primary indication for admission, clinical severity, oxygen supplementation level, vaccination and prior COVID-19 infection. Provincial and city-wide daily cases and reported deaths hospitalizations and excess deaths data were sourced from the NICD, the National Department of Health and the South African Medical Research Council. RESULTS Deaths and ICU admissions were 4.5% vs 21.3% (p<0.00001), and 1% vs 4.3% (p<0.00001); length of stay was 4.0 days vs 8.8 days; and mean age was 39 years vs 49 years for the Omicron and previous waves respectively. Admissions peaked and declined rapidly with peak bed occupancy at 51% of highest previous peak. Sixty two (63%) patients in COVID-19 wards had incidental COVID-19 following a positive SARS-CoV-2 PCR test . Only one third (36) had COVID-19 pneumonia, of which 72% had mild to moderate disease. The remaining 38% required high care or ICU admission. Fewer than half (45%) of patients in COVID-19 wards compared to 99.5% in the first wave required oxygen supplementation. City and provincial rates show decoupling of cases, hospitalisations and deaths compared to previous waves, corroborating the clinical findings of milder omicron disease in the hospital. CONCLUSION There was decreased severity of disease in the Omicron driven fourth wave in the City of Tshwane, its first global epicentre.
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Affiliation(s)
- F Abdullah
- Division of Infectious Diseases, Steve Biko Academic Hospital; Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria; South African Medical Research Council
| | - J Myers
- School of Public Health and Family Medicine, Faculty of Health Sciences, University of Cape Town
| | - D Basu
- Department of Public Health Medicine, University of Pretoria
| | - G Tintinger
- Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria
| | - V Ueckermann
- Division of Infectious Diseases, Steve Biko Academic Hospital; Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria
| | | | | | | | | | | | - J Cloete
- Department of Paediatrics, Steve Biko Academic Hospital and University of Pretoria
| | - P Soma-Pillay
- Department of Obstetrics, Steve Biko Academic Hospital and University of Pretoria
| | - P Rheeder
- Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria
| | - F Paruk
- Department of Critical Care, Steve Biko Academic Hospital and University of Pretoria
| | - A Engelbrecht
- Department of Emergency Medicine, Steve Biko Academic Hospital and University of Pretoria
| | - V Lalloo
- Department of Emergency Medicine, Steve Biko Academic Hospital and University of Pretoria
| | | | - J Kistan
- Department of Public Health Medicine, University of Pretoria
| | | | - M T Boswell
- Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria
| | - G Gray
- South African Medical Research Council
| | - R Welch
- National Institute of Communicable Diseases
| | - L Blumberg
- National Institute of Communicable Diseases; Right to Care, South Africa
| | - W Jassat
- National Institute of Communicable Diseases
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