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A 'relentless increase' in excess deaths from natural causes — SAMRC

The SA Medical Research Council's weekly analysis of registered deaths has shown a "relentless increase" on the number of excess deaths expected based on historical data, writes MedicalBrief.

The Medical Research Council (SAMRC) regularly produces the Report on Weekly Deaths in South Africa, published every Wednesday by the SAMRC’s Burden of Disease Research Unit. These reports include information on both natural (age, disease, infection) and unnatural deaths registered on the National Population Register.

The SAMRC says in the past weeks, the numbers have shown a relentless increase – by the second week of July, there were 59% more deaths from natural causes than would have been expected based on historical data. It also means that reported deaths have shown a pattern that is completely different to those indicated by historical trends.

According to Professor Debbie Bradshaw, chief specialist scientist and a co-author of the report, the timing and geographic pattern leaves no room to question whether this is associated with the COVID-19 epidemic. “However, the weekly death reports have revealed a huge discrepancy between the country’s confirmed COVID-19 deaths and number of excess natural deaths,” said Bradshaw.

In order to provide close to real time insight into changes in mortality, the Burden of Disease Research Unit collaborates with University of Cape Town’s Centre for Actuarial Research (CARe) to analyse the numbers of deaths registered by the Department of Home Affairs on the National Population Register, while providing weekly reports of the number of deaths in South Africa. Although done in some developed countries, South Africa is one of the few middle-income countries able to do this.

On lessons learnt in the context of COVID-19 in South Africa, Bradshaw says the weekly death reports have contributed important information to complement other data on the unfolding of the epidemic.

The report was able to confirm that no epidemics had occurred prior to the first COVID-19 cases identified by the National Institute for Communicable Diseases (NIICD) and the country’s first death announced by Health Minister, Dr Zweli Mkhize in March. It was through these reports that the early growth of the epidemic in Cape Town and the Western Cape was confirmed, followed by the spread in Nelson Mandela Bay and the Eastern Cape.

The surveillance also highlighted the rapid decrease in unnatural deaths with the implementation of a hard lockdown, and the return to usual numbers following the lifting of a hard lockdown and the restrictions on alcohol, with a sudden increase in the first week of June. The rise in numbers of deaths from natural causes in July in Gauteng has confirmed that the epidemic has set in the province.

Tracking weekly excess deaths is not a new phenomenon – several countries in the developed world have been reporting these trends, particularly to assess the impact of influenza. With the outbreak of the COVID-19 pandemic, more countries have started doing this. Such analyses have generally demonstrated that during the pandemic, countries experience excess numbers of deaths over and above confirmed COVID-19 deaths.

In the UK, for example, it was realised that the confirmed COVID-19 deaths reflected only the COVID-19 deaths that occurred in the health services and that deaths that occurred in long-term care institutions and at home were not included in their COVID-19 statistics. However, given the availability of cause of death data from the death registration process in the UK, they were able to add such deaths to their confirmed COVID-19 statistics. Nonetheless, there are still excess deaths over and above these COVID-19 deaths, which are assumed to be deaths from conditions that might normally have been diagnosed and treated had their hospitals not been overwhelmed.

Excess deaths are calculated in different ways. Some analysts take the excess above the expected number based on historical data while others take the number above a threshold such as the upper prediction bound – significantly higher than expected. In general, these excess deaths are calculated using all-cause mortality. It is considered that excess deaths would comprise COVID-19 deaths that are confirmed, COVID-19 deaths that have not been confirmed as well as other deaths that may arise from conditions that might normally have been diagnosed and treated had the public been willing and able to access health care.

Faced with the challenge that South Africa had a stringent lockdown in the very early stage of the epidemic and that unnatural deaths are a higher proportion of the all-cause mortality (and were impacted very significantly by the stringent lockdown), the SAMRC-UCT team thought it was necessary to use a different approach.

To quantify the impact of the COVID-19 epidemic on South African deaths, it was decided to focus on deaths from natural causes and remove the impact of changes in the unnatural deaths. The team also thought it would be necessary to consider that the lockdown had reduced the number of natural deaths. Thus, a baseline was chosen that was consistent with the level that the number of natural deaths was tracking prior to the uptick in the trend.

According to Professor Glenda Gray, SAMRC President and CEO, “the SAMRC has been tracking mortality for decades in South Africa, and this system has identified excess deaths associated with the COVID-19 epidemic. These may be attributed to both COVID-19 deaths as well non-COVID-19 due to other diseases such as TB, HIV and non-communicable diseases, as health services are re-orientated to support this health crisis.”


Until now, South Africa’s case fatality rate has suggested that while our numbers of infections are high, deaths had been perceived to be low because we are a country of largely young people. But, Daily Maverick reports, the MRC’s careful report, done in collaboration with the UCT’s Centre for Actuarial Research, has cast a new light and included analysis that extended beyond the institution’s weekly report on deaths in South Africa, which includes natural and unnatural deaths.

Excess deaths are those deaths that exceed the expected mortality trends established through the national weekly monitoring of deaths. Bradshaw said the timing and geographic patterns of the report leaves no room to question whether this is associated with COVID-19.

Many countries have been tracking excess death numbers to take a snapshot of the impacts of COVID-19. But Daily Maverick reports, back home, the tracking by the MRC and Bradshaw’s team was more complex as our system of death registration is different and less current.

This gets a bit tricky to read, but it is important to understand: “To quantify the impact of the COVID-19 epidemic on South African deaths, it was decided to focus on deaths from natural causes and remove the impact of changes in the unnatural deaths (accidents, traumas through violence, etc). The team also thought it would be necessary to consider that the lockdown had reduced the number of natural deaths.”

So, Daily Maverick says, what we see in the report is the rapid increase in natural deaths tracked in the National Population Register triangulated with known COVID-19 deaths to reveal an increase in excess of those. “The proportion is calculated such that the excess deaths in that week is equal to the confirmed number of COVID-19 deaths for that week. The cumulative number of excess deaths comprises the sum of the weekly excess plus the cumulative number of confirmed deaths prior to the establishment of a clear upward trend.”


South Africa’s health minister has downplayed the possible under-reporting of COVID-19 deaths, Daily Maverick reports. Being a politically astute politician – this savviness goes back to his days as premier of a fractious KwaZulu-Natal – the report says it was unlikely that Mkhize would not respond to the SAMRC reporting a 59% rise in excess natural deaths between May and July compared to historical data.

The possibility of COVID-19 deaths not being accurately recorded would raise yet another spectre in a flailing health system already dealing with crises over a lack of beds, oxygen supplies and personal protective equipment. In addition, there are questions over delays of up to nine days in coronavirus test results and the tracing of contacts of COVID-19 patients.

“Their (the SAMRC’s) findings reveal that there may be additional deaths which are unaccounted for based on the modelling which they have done. It has also been acknowledged that there is uncertainty about the exact number of excess deaths in these circumstances,” said Mkhize at the Health Special Adjustment Budget vote debate in Parliament.

Daily Maverick says he provided explanations such as people dying of COVID-19 before getting to hospital, COVID-19 deaths not being reported as such and people dying from non-COVID-19 causes because health services have been “re-orientated” for the pandemic.

“However, in comparison to other countries, as at 18 July 2020, South Africa recorded 1.4% of deaths, which is comparable to countries like India at 2.5 and Russia at 1.5, but significantly lower than countries like the UK at 15.4%, Spain at 10.9% and the US at 3.88. We will continue to analyse this trend.”

Mkhize told MPs all provinces were urged to report COVID-19 deaths as soon as possible to avoid the backlog that, in turn, may create what the minister called “a confusing and concerning perception that there is under-reporting of COVID-19 deaths”.


[link url="–samrc"]Full report on the Politicsweb site[/link]


[link url=""]SAMRC weekly report[/link]


[link url=""]Full Daily Maverick report[/link]


[link url=""]Full Daily Maverick report[/link]

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