Study design
We implemented a retrospective cohort analysis of SARS-CoV-2 positive cases in LTCFs across South Africa from 5 March 2020 – 31 July 2021.
Data source
DATCOV, a hospital surveillance system for COVID-19 admissions, was initiated on 1 April 2020 and then subsequently expanded to include sentinel surveillance in LTCFs, implemented on 4 June 2020. Data are submitted by LTCFs that have agreed to report COVID-19 cases via the DATCOV LTCFs module. Participation in the LTCFs surveillance was voluntary and included a small number of sentinel facilities. When new facilities enrolled, they captured historical cases going back to their first recorded SARS-CoV-2 case.
Definitions of LTCFs
A range of LTCFs or congregate settings were included in the sentinel surveillance, including old age homes (21, 46.7%), retirement villages (11, 24.4%), mental health facilities (7, 15.6%), substance abuse recovery facilities (4, 8.9%) and frail care facilities 2 (4.4%). An old age home is defined as a LTCF where residents require daily care in a comfortable, safe and active environment.9 Retirement villages are defined as accommodating places that provide an independent lifestyle for those who do not need additional living assistance.10 A frail care centre is defined as a place giving care to those who are unable to care for themselves as a result of a motor-vehicle accident, physical disability, severe stroke or old age.9 Psychiatric and mental hospitals are defined as specialized hospital-based facilities that provide inpatient care and long-stay residential services for people with mental disorders.9 These facilities are usually independent and stand-alone, although they may have some links with the rest of the healthcare system. Substance abuse rehabilitation treatment facilities are defined as centres rectifying maladaptive behaviours and providing help with recovery from substance abuse disorders.11
Study population
The study population included all LTCF residents and staff in participating LTCFs in South Africa.
For the purpose of this study, we defined outbreaks in a LTCF as follows: 12
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A sporadic case is defined as a single laboratory confirmed case of SARS-CoV-2 with 14-day period or longer before another laboratory-confirmed case.
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A small outbreak was defined as 2 to 20 confirmed SARS-CoV-2 cases or less than one third of residents or staff of a LTCF infected, within a 14-day period, with an epidemiological link.
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A large outbreak was defined as >20 confirmed SARS-CoV-2 cases or more than one third of residents or staff of a LTCF infected, within a 14-day period, with an epidemiologic link.
The wave periods were defined by the case incidence data with a national weekly incidence of 30 cases per 100,00013 as cut off for start and end of wave periods:
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Pre-wave-1: epidemiologic weeks 10 – 23 of 2020 (1 March – 6 June 2020)
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First wave: epidemiologic weeks 24 – 34 of 2020 (7 June – 22 August 2020)
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Post-wave 1: epidemiologic weeks 35 – 46 of 2020 (23 August – 14 November 2020)
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Second wave: epidemiologic weeks 47 of 2020 – week 5 of 2021 (15 November 2020 – 06 February 2021)
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Post-wave 2: epidemiologic weeks 6 – 19 of 2021 (7 February – 8 May 2021)
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Third wave: epidemiologic weeks 20 – 30 of 2021 (09 May 2021 – 31 July 2021)
Data collection and management
Data collection was either through direct entry onto the DATCOV online platform or through importation of electronic data via bulk-upload for LTCFs that did not have a stable internet connection. If a resident or staff member tested positive for SARS-CoV-2, the dedicated data entry clerk in the LTCF would complete the electronic data form. The case reporting form was adapted from the World Health Organisation (WHO) SARS-CoV-2 case reporting tool and included basic demographic data, pre-existing health conditions and outcomes (died and recovered).
Data imports contained validation checks to identify data errors. Routine checks were performed on all data. Missing and discrepant data were followed up telephonically or by email with the submitting person.
COVID-19 mortality was defined as a death related to SARS-CoV-2 that occurred at the LTCF or while being admitted to hospital, excluding deaths that occurred due to other causes or after recovery. A COVID-19 death is defined for surveillance purposes as a death due to a clinically compatible illness, in a confirmed COVID-19 case, unless there is a clear alternative cause of death that cannot be related to COVID disease (e.g. trauma), with no period of complete recovery from COVID-19 between illness and death.14
Data analysis
Descriptive statistics including frequencies and percentages were used for categorical variables, while for continuous variables a median and interquartile range (IQR) were calculated.
A random effect multivariable logistic regression model was used to assess risk factors for mortality amongst LTCF residents with laboratory-confirmed SARS-CoV2. Age, race, sex and comorbidities (hypertension, diabetes mellitus, chronic cardiac disease, asthma, other chronic respiratory disease, chronic renal disease, malignancy in the past five years, HIV, past and current tuberculosis), smoking, obesity, province, type of LTCF, and wave period, were included in models assessing risk factors for COVID-19 mortality. We assessed all variables that were significant at p<0.2 on univariate analysis and dropped non-significant factors (p≥0.05) with manual backward elimination. Pairwise interactions were assessed by inclusion of product terms for all variables remaining in the final multivariable additive model. We also reported the univariate association of all covariates evaluated in the analyses described above to the main outcome (mortality in individuals with COVID-19). The statistical analysis was implemented using Stata 15 (Stata Corp®, College Station, Texas, USA).
Ethical considerations
The data used for this study were de-identified to ensure confidentiality. All personal information of the residents and staff, concerning health status, treatment or stay in a health establishment, were kept confidential and stored in a secure server. For analysis, patient identifiers were de-linked from other data and stored separately. Ethical approval for this study was obtained from the University of the Witwatersrand Human Research Ethics Committee (M160667). The study was performed in accordance with all relevant ethical guidelines and regulations and with good clinical practice.
Disease surveillance is a critical function of the NICD as a statutory body in South Africa. The NICD has a national mandate to conduct COVID-19 hospital surveillance. The amended regulations that accompany the declaration of a national disaster (Disaster Management Act 2002), provides for healthcare institutions to submit data to NICD on notifiable medical conditions, which includes COVID-19. This encompasses the submission of patient details, their treatment and outcomes. In this case individual consent is therefore waived.