a SARS-CoV-2 variant of concern, Omicron (B.1.1.529), was identified in South Africa as responsible for a fourth wave of COVID-19. 1,2 The high number of spike mutations has raised concerns about its ability to evade vaccine and spread. 3,4 We assessed hospitalized patients with a positive SARS-CoV-2 test result during the fourth wave compared with previous waves.Methods | Netcare is a private health care group consisting of 49 acute care hospitals (>10 000 beds) across South Africa. South Africa has experienced 3 COVID-19 waves: (1) June to August 2020 (ancestral variant), (2) November 2020 to January 2021 (Beta), and (3) May to September 2021 (Delta). Cases again started to increase beginning November 15, 2021, coinciding with the identification of Omicron; as of December 7, 26% community positivity rates were reached. We identified the period when 26% positivity rates were reached in the previous waves (wave 1:

Background The interaction between COVID-19, non-communicable diseases, and chronic infectious diseases such as HIV and tuberculosis is unclear, particularly in low-income and middle-income countries in Africa. South Africa has a national HIV prevalence of 19% among people aged 15-49 years and a tuberculosis prevalence of 0•7% in people of all ages. Using a nationally representative hospital surveillance system in South Africa, we aimed to investigate the factors associated with in-hospital mortality among patients with COVID-19. MethodsIn this cohort study, we used data submitted to DATCOV, a national active hospital surveillance system for COVID-19 hospital admissions, for patients admitted to hospital with laboratory-confirmed SARS-CoV-2 infection between March 5, 2020, and March 27, 2021. Age, sex, race or ethnicity, and comorbidities (hypertension, diabetes, chronic cardiac disease, chronic pulmonary disease and asthma, chronic renal disease, malignancy in the past 5 years, HIV, and past and current tuberculosis) were considered as risk factors for COVID-19-related in-hospital mortality. COVID-19 in-hospital mortality, the main outcome, was defined as a death related to COVID-19 that occurred during the hospital stay and excluded deaths that occurred because of other causes or after discharge from hospital; therefore, only patients with a known in-hospital outcome (died or discharged alive) were included. Chained equation multiple imputation was used to account for missing data and random-effects multivariable logistic regression models were used to assess the role of HIV status and underlying comorbidities on COVID-19 in-hospital mortality. FindingsAmong the 219 265 individuals admitted to hospital with laboratory-confirmed SARS-CoV-2 infection and known in-hospital outcome data, 51 037 (23•3%) died. Most commonly observed comorbidities among individuals with available data were hypertension in 61 098 (37•4%) of 163 350, diabetes in 43 885 (27•4%) of 159 932, and HIV in 13 793 (9•1%) of 151 779. Tuberculosis was reported in 5282 (3•6%) of 146 381 individuals. Increasing age was the strongest predictor of COVID-19 in-hospital mortality. Other factors associated were HIV infection (adjusted odds ratio 1•34, 95% CI 1•27-1•43), past tuberculosis (1•26, 1•15-1•38), current tuberculosis (1•42, 1•22-1•64), and both past and current tuberculosis (1•48, 1•32-1•67) compared with never tuberculosis, as well as other described risk factors for COVID-19, such as male sex; non-White race; underlying hypertension, diabetes, chronic cardiac disease, chronic renal disease, and malignancy in the past 5 years; and treatment in the public health sector. After adjusting for other factors, people with HIV not on antiretroviral therapy (ART; adjusted odds ratio 1•45, 95% CI 1•22-1•72) were more likely to die in hospital than were people with HIV on ART. Among people with HIV, the prevalence of other comorbidities was 29•2% compared with 30•8% among HIV-uninfected individuals. Increasing number of comorbidities was associated with...

Background The first wave of COVID-19 in South Africa peaked in July, 2020, and a larger second wave peaked in January, 2021, in which the SARS-CoV-2 501Y.V2 (Beta) lineage predominated. We aimed to compare in-hospital mortality and other patient characteristics between the first and second waves.Methods In this prospective cohort study, we analysed data from the DATCOV national active surveillance system for COVID-19 admissions to hospital from March 5, 2020, to March 27, 2021. The system contained data from all hospitals in South Africa that have admitted a patient with COVID-19. We used incidence risk for admission to hospital and determined cutoff dates to define five wave periods: pre-wave 1, wave 1, post-wave 1, wave 2, and post-wave 2. We compared the characteristics of patients with COVID-19 who were admitted to hospital in wave 1 and wave 2, and risk factors for in-hospital mortality accounting for wave period using random-effect multivariable logistic regression.Findings Peak rates of COVID-19 cases, admissions, and in-hospital deaths in the second wave exceeded rates in the first wave: COVID-19 cases, 240•4 cases per 100 000 people vs 136•0 cases per 100 000 people; admissions, 27•9 admissions per 100 000 people vs 16•1 admissions per 100 000 people; deaths, 8•3 deaths per 100 000 people vs 3•6 deaths per 100 000 people. The weekly average growth rate in hospital admissions was 20% in wave 1 and 43% in wave 2 (ratio of growth rate in wave 2 compared with wave 1 was 1•19, 95% CI 1•18-1•20). Compared with the first wave, individuals admitted to hospital in the second wave were more likely to be age 40-64 years (adjusted odds ratio [aOR] 1•22, 95% CI 1•14-1•31), and older than 65 years (aOR 1•38, 1•25-1•52), compared with younger than 40 years; of Mixed race (aOR 1•21, 1•06-1•38) compared with White race; and admitted in the public sector (aOR 1•65, 1•41-1•92); and less likely to be Black (aOR 0•53, 0•47-0•60) and Indian (aOR 0•77, 0•66-0•91), compared with White; and have a comorbid condition (aOR 0•60, 0•55-0•67).For multivariable analysis, after adjusting for weekly COVID-19 hospital admissions, there was a 31% increased risk of in-hospital mortality in the second wave (aOR 1•31, 95% CI 1•28-1•35). In-hospital case-fatality risk increased from 17•7% in weeks of low admission (<3500 admissions) to 26•9% in weeks of very high admission (>8000 admissions; aOR 1•24, 1•17-1•32).Interpretation In South Africa, the second wave was associated with higher incidence of COVID-19, more rapid increase in admissions to hospital, and increased in-hospital mortality. Although some of the increased mortality can be explained by admissions in the second wave being more likely in older individuals, in the public sector, and by the increased health system pressure, a residual increase in mortality of patients admitted to hospital could be related to the new Beta lineage.

Background The COVID-19 pandemic caused severe disruptions to healthcare in many areas of the world, but data remain scarce for sub-Saharan Africa. Methods We evaluated trends in hospital admissions and outpatient emergency department (ED) and general practitioner (GP) visits to South Africa’s largest private healthcare system during 2016 – 2021. We fit time series models to historical data and, from March 2020 to September 2021, quantified changes in encounters relative to baseline. Results The nationwide lockdown on 26 March 2020 led to sharp reductions in care-seeking behavior that persisted for 18 months after initial declines. For example, total admissions dropped 59.6% [95% confidence interval: 52.4, 66.8] during home confinement and were 33.2% [29, 37.4] below baseline in September 2021. We identified three waves of all-cause respiratory encounters consistent with COVID-19 activity. Intestinal infections and non-COVID-19 respiratory illnesses experienced the most pronounced declines, with some diagnoses reduced 80%, even as non-pharmaceutical interventions (NPIs) were relaxed. Non-respiratory hospitalizations, including injuries and acute illnesses (e.g., heart attack, stroke), were 20-60% below baseline throughout the pandemic and exhibited strong temporal associations with NPIs and mobility behavior. ED attendances exhibited similar trends to hospitalizations, while GP visits, particularly for chronic illnesses and HIV, were less impacted and have returned to pre-pandemic levels. Conclusions We find substantially reduced use of health services during the pandemic for a range of conditions unrelated to COVID-19. Persistent declines in hospitalizations and ED visits indicate that high-risk patients are still delaying seeking care, which could lead to morbidity or mortality increases in the future.

Background South Africa has experienced two waves of COVID-19 infections, the second of which was inter alia attributed to the emergence of a novel SARS-CoV2 variant, 501Y.V2. This variant possibly has increased virulence and may be associated with increased mortality. The objective of this study was to determine if patients admitted in the second wave had more severe illness and higher mortality than those admitted in the first. Methods We analysed and compared the characteristics, biological severity markers, treatments, level of care and outcomes of patients hospitalised in a private hospital in the Eastern Cape Province, South Africa. Results Compared to the first wave, patients admitted in the second were older and less likely to have co-morbidities. In contrast, the D-dimer and interleukin-6 (IL-6) levels were significantly higher. Despite this, significantly less patients were admitted to ICU and/or were mechanically ventilated. The total length of hospital stay was identical in both groups. Whereas the overall mortality was not significantly higher during the second wave, the ICU mortality was. Those that died in the second wave were older than those in the first wave. Multivariable logistic regression showed that being admitted during the second wave was an independent risk factor for mortality. Conclusion This study appears to confirm previous reports that the 501Y.V2 variant is possibly more virulent as indicated by the higher levels of D-dimer and IL-6, the slight increase in mortality of hospitalised patients and the higher ICU mortality in the second wave.