SARS-CoV-2 Cases Reported in Long-Term Residential Facilities (Nursing Homes) in South Africa: A Retrospective Cohort Study – BMC Public Health

As of July 31, 2021, 2,324 cases of SARS-CoV-2 have been reported from 45 long-term care facilities in eight of South Africa’s nine provinces. Psychiatric facilities reported the most cases (918, 39.5%), followed by nursing homes (420, 18.1%), retirement villages (405, 17.4%), drug rehabilitation centers ( 391, 16.8%) and care facilities for frail people (190, 8.2%).

Psychiatric facilities reported cases in 657/1504 (43.8%) residents and 261/8201504 (31.8%) staff; nursing homes reported 269/1504 (17.9%) residents and 151/820 (18.4%) staff infected, drug treatment centers 241/1504 (16.0%) residents and 150/820 (18.3% ) staff infected, retirement villages 214/1504 (14.2%) residents and 191/820 (23.3%) staff members infected; and fragile care centers 123/1504 (8.2%) residents and 67/820 (8.2%) staff infected (Fig. 1 a).

Of all SARS-CoV-2 cases from sentinel ELDs, 1,259 (54.2%) were reported in the first wave, 362 (15.6%) in the second wave, and 299 (12.9 %) during the third wave (Fig. 2).

Temporal trend of SARS-CoV-2 cases in LTCFs in LTCFs

The proportion of cases among staff decreased during the surveillance period (Fig. 1 b).

Pattern of outbreaks in long-term care facilities

There were varying patterns of outbreaks among long-term care facilities, with six (13.3%) reporting no outbreaks (only sporadic cases), 10 (22.2%) reporting an outbreak, and 29 ( 64.5%) reporting more than one outbreak (Supplementary Table 1). The six long-term care facilities (13.3%) reporting sporadic SARS-CoV-2 positive cases included four retirement homes and two retirement villages (Supplementary Figure a). There were 48 (66.7%) small outbreaks and 24 (33.3%) large outbreaks reported (Supplementary figure b). The 24 (61.5%) long-term care facilities that reported large SARS-CoV-2 outbreaks included 8 (33.3%) retirement villages, 6 (25.0%) psychiatric facilities, 5 ( 20.8%) retirement homes, 4 (16.7%) detox centers. and 1 (4.0%) care center for frail people (Supplementary figure c). There were 30 outbreaks reported in wave 1, 21 in wave 2 and 15 in wave 3, while 6 outbreaks were reported between waves.

Demographic and clinical characteristics of SARS-CoV-2 cases among LTCF residents

The median age of COVID-19 cases among residents was 56 years (IQR 38–73) and 812/1504 (54.0%) were male (Table 1). Of the 1,501 (99.8%) residents whose race was known, 734 (49.0%) were black African, 610 (40.6%) were white, 101 (6.7%) were colored and 56 ( 3.7%) were Indian. Of the 1473 (97.9%) residents for whom there was data on comorbidities, 274 (18.6%) had comorbidities. Of these, 191 (69.7%) had one comorbid condition, 60 (21.9%) had two comorbid conditions, and 23 (8.3%) had three or more comorbid conditions. The most common comorbid conditions among residents were hypertension (194, 15.2%), diabetes mellitus (64, 4.5%) and chronic heart disease (48, 3.4%). Of the 1504 SARS-CoV-2 positive residents with results, 1308 (87.0%) recovered, 59 (3.9%) were active cases and 137 (9.1%) had died, which gives a case fatality rate (CFR) of 9.1%. The CFR excluding active cases among residents was 137/1445 (9.5%).

Demographic and clinical characteristics of SARS-CoV-2 cases among LTCF staff

The median age of COVID-19 admissions among staff was 42 (IQR 35–51) and 705/820 (86.0%) were female (Table 1). Of the 767 (93.5%) staff whose race was known, 640 (83.4%) were black African, 79 (10.3%) were mixed race, 8 (1.0%) were Indian and 40 (5.2%) were white. Of the 793 (96.7%) staff members for whom there was comorbidity data, 104 (13.1%) had comorbidities. Of these, 82 (78.8%) had one comorbid condition, 20 (18.2%) had two, and three (2.9%) had three or more comorbid conditions. The most common comorbidities among staff were hypertension 69 (8.7%), diabetes mellitus 28 (3.5%), HIV 15 (1.9%) and asthma 14 (1.8%). ). Of the 820 SARS-CoV-2 positive staff with results, 762 (92.9%) cases recovered, 54 (6.6%) were active cases and 4 (0.5%) had died , giving a case fatality rate (CFR) of 0.5%. The CFR excluding active cases among staff was 4/766 (0.5%).

Temporal trend of SARS-CoV-2 deaths in long-term care facilities

The number of SARS-CoV-2 and CFR deaths among residents in the different epidemic periods was 22/115 (19.1%) in pre-wave 1; 72/793 (9.1%) in wave 1; 5/60 (8.3%) post-wave 1; 23/241 (9.5%) in wave 2, 4/18 (22.2%) in post-wave 2 and 16/218 (7.3%) in wave 3. (Fig. 3).

The number of SARS-CoV-2 deaths and CFRs among staff during the different pandemic periods was 1/91 (1.1%) during pre-wave 1; 2/438 (0.5%) in wave 1; and 1/112 (0.9%). No deaths occurred among satff during post-wave 1, post-wave 2 and wave 3.

Among residents, the CFR was 46/252 (18.3%) in retirement homes, 15/112 (13.4%) in care centers for frail people; 21/389 (10.5%) in retirement villages; 47/649 (7.2%) in psychiatric institutions; and 9/232 (3.9%) in drug treatment centers.

Of the four staff members (0.5%) who died, two were female and two were male. The median age was 48.5 years (IQR 44.5–57.0). A woman suffered from hypertension and diabetes mellitus. The other three who died had no reported comorbidities. Each of the four deaths occurred at a nursing home, mental institution, retirement village and drug rehabilitation centre.

Factors associated with SARS-CoV-2 mortality among residents

In multivariable analysis, factors associated with SARS-CoV-2 mortality among residents of long-term care facilities were aged 40 to 59 years (aOR 2.4, 95% CI 1.0 to 5.5 ), 60–79 years (aOR 7.6, 95% CI 3.6–16.5), and ≥ 80 years (aOR 18.2, 95% CI 8.1–41.2) compared to < 40 years; and being a resident of an LTCF in the Free State (aOR 4.2, 95% CI 1.4-12.8) or in the Northern Cape (aOR 3.8, 95% CI 1.2-12, 6) compared to the Western Cape (table 2). Compared to pre-wave 1, there was a decreased risk of mortality in wave 1 (aOR 0.3, 95% CI 0.1-0.9), after wave 1 (aOR 0.2 , 95% CI 0.05-0.8), wave 2 (aOR 0.3, 95% CI 0.1–1.0), after wave 2 (aOR 0.1, 95% CI 0, 02–0.9) and wave 3 (aOR 0.2, 95% CI 0.006–0.6).

Table 2 Multivariate analysis of factors associated with SARS-CoV-2 mortality among residents of long-term care facilities, South Africa, 5 March 2020–31 July 2021 (not= 1504).