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MRC: Eastern Cape COVID-19 deaths 'vastly underestimated'

The Eastern Cape, Limpopo, Mpumalanga and KwaZulu-Natal have had the highest proportion of deaths from COVID-19 cases to date, with case fatality rates exceeding the national in-hospital average of 22%. The Times reports that this is according to University of the Witwatersrand (Wits) epidemiology professor Cheryl Cohen.

Provincial case fatality rates for hospitalised patients are as follows: Eastern Cape 32%, Limpopo 29%, Mpumalanga 25%, KwaZulu-Natal 24%, Free State 22%, Gauteng 20%, Northern Cape 19%, Western Cape 18% and North West 14%.

Private hospitals had a lower case fatality rate (18%) than the public in-hospital rate of 25% said Cohen, co-head of the Centre for Respiratory Disease and Meningitis at the National Institute for Communicable Diseases (NICD).

An audit was under way “to better describe the factors associated with mortality in the facilities with highest case fatality rates across the country”, she said.

Dr Gesine Meyer-Rath, a health economist and infectious disease modeller at Wits Health Economics and Epidemiology Research Office, is quoted in The Times report as saying that the provinces reported differently on deaths in and outside hospitals.

In many smaller provinces responses to COVID-19 had been excellent, while one of the biggest provinces, the Eastern Cape, had fared worst with regard to the mortality rate she said.


A team of scientists at the NICD have released a study on the mortality rate among patients hospitalised with COVID-19 during the second wave.

When a second wave of infections swept across the globe, most countries reported a rise in cases, but a lower case-fatality risk (CFR). The outcomes evoked a sense of cautious optimism, that can in part be attributed to better patient treatment, increased testing capacity and improved preparedness of health care systems. When the second wave hit South Africa, peaking in January 2021, the new variant (SARS-CoV-2 501Y.V2) was identified as the leading contributor of the rapid rise in infections. Although the severity of 501Y.V2 is yet to be determined, some data do suggest increased transmissibility between individuals.

In an effort to understand the rate of mortality during the second wave, NICD scientists analysed data from DATCOV, a National Hospital Surveillance System that enabled public and private hospitals to submit data on all COVID-19 hospital admissions. The team compared in-hospital mortality, and other patient characteristics between the first and second waves of COVID-19.

The study revealed that in-hospital mortality increased with more patients being admitted for COVID-19. It furthermore showed that in-hospital case fatality-risk (CFR) increased from 17.9% in the weeks of low COVID-19 admission numbers (<3,500 admissions) to 29.6% in the weeks of very high occupancy. Importantly, even after accounting for the effects of the increased load of COVID-19 hospital patients, there was an additional 20% risk of in-hospital mortality (in the second wave) which could possibly be related to the new variant.

The data ultimately suggests that the 501Y.V2 lineage may be associated with higher in-hospital mortality compared to old lineages. However, the data should be interpreted with caution as the team did not have individual level data on who was infected with the new or old lineages. And other factors could have changed from the first to the second wave period. Individual level studies, comparing the outcomes of those with and without the new lineage, based on sequencing data, is needed.

In essence, to prevent increased mortality in a potential third wave, a combination of strategies is required to slow the transmission pace of SARS-CoV-2, to help flatten the peak of the epidemic. This will relieve pressure on our healthcare systems and enable hospitals to prepare for surge capacity (thereby avoiding breaching capacity), with the hopes of decreased mortality figures.


Study details
Increased mortality among individuals hospitalised with COVID-19 during the second wave in South Africa

Waasila Jassat, Caroline Mudara, Lovelyn Ozougwu, Stefano Tempia, Lucille Blumberg, Mary-Ann Davies, Yogan Pillay, Terrence Carter, Rams Morewane, Milani Wolmarans, Anne von Gottberg, Jinal N Bhiman, Sibongile Walaza, DATCOV Author Group, Cheryl Cohen

Published in medRxiv on 9 March 2021

South Africa experienced its first wave of COVID-19 peaking in mid-July 2020 and a larger second wave peaking in January 2021, in which the SARS-CoV-2 501Y.V2 lineage predominated. We aimed to compare in-hospital mortality and other patient characteristics between the first and second waves of COVID-19.
We analysed data from the DATCOV national active surveillance system for COVID-19 hospitalisations. We defined four wave periods using incidence risk for hospitalisation, pre-wave 1, wave 1, pre-wave 2 and wave 2. We compared the characteristics of hospitalised COVID-19 cases in wave 1 and wave 2, and risk factors for in-hospital mortality accounting for wave period using multivariable logistic regression.
Peak rates of COVID-19 cases, admissions and in-hospital deaths in the second wave exceeded the rates in the first wave (138.1 versus 240.1; 16.7 versus 28.9; and 3.3 versus 7.1 respectively per 100,000 persons). The weekly average incidence risk increase in hospitalisation was 22% in wave 1 and 28% in wave 2 [ratio of growth rate in wave two compared to wave one: 1.04, 95% CI 1.04-1.05]. On multivariable analysis, after adjusting for weekly COVID-19 hospital admissions, there was a 20% increased risk of in-hospital mortality in the second wave (adjusted OR 1.2, 95% CI 1.2-1.3). In-hospital case fatality-risk (CFR) increased in weeks of peak hospital occupancy, from 17.9% in weeks of low occupancy (<3,500 admissions) to 29.6% in weeks of very high occupancy (>12,500 admissions) (adjusted OR 1.5, 95% CI 1.4-1.5).
Compared to the first wave, individuals hospitalised in the second wave, were more likely to be older, 40-64 years [OR 1.1, 95% CI 1.0-1.1] and ≥65 years [OR 1.1, 95% CI 1.1-1.1] compared to <40 years; and admitted in the public sector [OR 2.2, 95% CI 1.7-2.8]; and less likely to have comorbidities [OR 0.5, 95% CI 0.5-0.5].
In South Africa, the second wave was associated with higher incidence and more rapid increase in hospitalisations, and increased in-hospital mortality. While some of this is explained by increasing pressure on the health system, a residual increase in mortality of hospitalised patients beyond this, could be related to the new lineage 501Y.V2.


An investigation into the high COVID-19 fatality rate in the Eastern Cape has shown that about 40% of patients who died had comorbidities and succumbed to the disease in hospital casualty wards or within 48 hours of being admitted, says a Daily Maverick report.

The latest official epidemiological report issued for the outbreak in the province also conceded that the deaths caused by COVID-19 in the province have been “vastly understated”, as has the positivity rate in parts of the Eastern Cape. The report raises the issue that a high positivity rate found during post-mortem testing in the province indicates that there are a “high number” of COVID-19 related deaths that are not being reported.

The Medical Research Councils (MRC) excess death report has put the cumulative excess deaths at 502/100,000, – double the national excess death rate. According to the MRC, 33,072 people died between May 2020 and 13 March 2021 in the Eastern Cape

“Although more data are needed on the underlying causes of death, this observation is strongly supportive that a significant proportion of the current excess mortality being observed in South Africa is likely to be attributable to COVID-19,” the MRC stated in its latest report.

The province has a case fatality rate of 6% at present, meaning that 6% of those diagnosed with COVID-19 died. The Chris Hani district, including districts in the former homelands of the Ciskei and Transkei, and the area around Komani (Queenstown), Cradock and Middelburg has the province’s highest case fatality rate at 7.9%.

In February 2021, the case fatality rates in the province had doubled to 12%.

DM reports that with the department finding itself in deepening financial trouble, doctors have raised the concern that cutting equipment budgets will make the situation worse if a third wave hits the province.

Eastern Cape Health Department spokesperson Sizwe Kupelo said the analysis of COVID-19 deaths by the department’s Dr Nokuzola Ntlangula found that 40% of patients who died, died either in hospitals’ casualty wards or within 48 hours after admission. He said they found that many of these patients had comorbidities.



Full report in The Times (Open access)

NICD Weekly Epidemiological Report

NICD material

medRxiv study (Restricted access)

Full Daily Maverick report (Open access)

SAMRC Excess Deaths report

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