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Researchers find 'huge discrepancy' between reported number of Covid-19 fatalities and excess deaths

  • An estimated 17 090 more natural deaths than expected between 6 May and 14 July has raised concern about the accuracy of reported Covid-19 deaths.
  • Excess mortality is a measure used internationally to decipher actual deaths during large-scale epidemics.
  • It remains unclear why so many South Africans are dying, if it is not related to Covid-19.


South Africans are dying at a much higher rate than expected as Covid-19 continues to spread at a significant pace in at least three provinces.

Excess deaths between 6 May and 14 July topped 17 000, according to the latest research by the South African Medical Research Council (SAMRC) and University of Cape Town's Centre for Actuarial Research.

"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," the SAMRC said in a statement on Wednesday.

Professor Debbie Bradshaw, a co-author of the report, said 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 the number of excess natural deaths," she added.

As of 21 July, the number of confirmed Covid-19 deaths was 5 368.

Key takeaways from the latest report for excess mortality up to 14 July:

  • Between 6 May and 14 July, excess deaths from natural causes were 17 090 for persons one year and older.
  • For people between the ages of one and 59, the excess number of deaths is 5 889 and 11 175 for people 60 and older.
  • The Western Cape, Eastern Cape, Gauteng and KwaZulu-Natal are experiencing excess natural deaths. These are the hardest-hit provinces in terms of confirmed Covid-19 deaths and cases.
  • Mpumalanga, the Free State, Limpopo and North West have also started showing increases in excess deaths from natural causes.


Graph showing number of natural deaths

The number of natural deaths, weekly, nationally. (Source: SAMRC-UCT Weekly Mortality Report 22 July 2020).

The authors of the weekly report include Bradshaw, Ria Laubscher, Professor Rob Dorrington, Professor Pam Groenewald and Professor Tom Moultrie who, together and individually, comprise a highly accomplished and qualified team of some of the country's foremost experts in demography, statistics and mortality.

Professor Glenda Gray, the CEO and president of the SAMRC, said the council had been tracking mortality for decades.

"This system has identified excess deaths associated with the Covid-19 epidemic. These may be attributed to both Covid-19 deaths as well as 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," she added.

Excess deaths

The excess is calculated using the number of reported deaths from the National Population Register (NPR), which is maintained by the Department of Home Affairs. A forecast is calculated based on the number of deaths reported from natural and unnatural causes in past years.

The forecast is also calculated with an upper and lower expectation bound.

The team then uses documented weighting methods to account for multiple variables that could affect the true number of deaths other than what is reported in the NPR data.

According to the SAMRC, there were different ways in which excess deaths were calculated.

"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 i.e. significantly higher than expected," the SAMRC said in a statement on Wednesday.

"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."

Table showing estimated excess deaths

Table showing estimated excess deaths as at 14 July. (Source: SAMRC-UCT Weekly Mortality Report 22 July 2020).



In an information sheet shared along with the latest report, the authors acknowledge there was uncertainty about the exact number of excess deaths. They said the uncertainty arose from having to estimate not only the actual number of deaths, but also what would have happened without the Covid-19 pandemic.

"We have reported the challenges that we face and the method that we have used. Our estimate excess natural deaths could be revised should an improved method be identified.

"However, given the timing and geographic spread of the increases seen in the natural deaths, there can be no doubt that the bulk of the increase is related directly or indirectly to Covid-19."

The authors consider the gap between the number of excess deaths and confirmed Covid-19 deaths probably comprises:

  • People dying from Covid-19 before they get to a healthcare facility.
  • People dying from Covid-19 but the death not being reported as such.
  • People dying from non-Covid-19 conditions because health systems have been orientated to Covid-19 patients.

Testing constraints in the public sector also mean many cases are being picked up only when people arrive at healthcare facilities.


"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," the SAMRC statement read.

The SAMRC said: 

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."

Bradshaw said 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 (NICD) 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."

As of 14 July, the number of deaths from unnatural causes such as car accidents and murders was 20% below expected totals.

Graph showing number of unnatural deaths weekly

The number of unnatural deaths weekly. (Source: SAMRC-UCT Weekly Mortality Report 22 July 2020).

 Kyle Cowan



Spur's restaurant sales plunged over 80% since the start of lockdown

All the restaurant chains in Spur Corporation's stable have reported massive drops in sales during May and June due to the nationwide lockdown. 

Spur owns Spur Steak Ranches, Italian food franchise Panarottis, seafood restaurant John Dory's, burger joint RocoMamas and steak restaurant Hussar Grill.

Sales plummeted by 87.2% in May and 83.6% in June, according to a trading update released on Thursday.

SA restaurants were able to recommence trading on a delivery-only basis at the start of May, with a collection permitted from June 1, 2020. Sit-down services resumed on June 29. 

Earlier in the week Spur's longtime CEO, Pierre van Tonder, handed in his resignation after leading the restaurant group for 24 years, saying the Covid-19 pandemic is worse than the global financial crisis. 


Anathi Madubela



Cabinet to be told to close schools for 3 weeks amid Covid-19 peak - report

  • Cabinet is expected to be advised to close schools across South Africa for three weeks.
  • The announcement will be tabled on Thursday, with an announcement expected soon thereafter.
  • This as teachers' unions have been engaging with government to close schools amid a surge in Covid-19 infections.



The National Coronavirus Command Council (NCCC) is expected to advise Cabinet to close schools around the country for three weeks.

This according to a report by Times LIVE, which quotes "impeccable sources within the teacher unions" who attended a meeting chaired by Deputy Minister of Basic Education Reginah Mhaule on Wednesday night.

The NCCC will reportedly table the recommendation to Cabinet on Thursday, and either Basic Education Minister Angie Motshekga or President Cyril Ramaphosa will then announce Cabinet's decision.

Department spokesperson Elijah Mhlanga told News24 consultations with the sector's stakeholders were continuing ahead of another Cabinet meeting scheduled for Thursday.

Motshekga is expected to give feedback to Cabinet on Thursday before an announcement is made.

According to Times LIVE's sources, Cabinet will finalise the matter on Thursday.

"What prevails now is three weeks on the table," a source reportedly said.

 'Anxiety and uncertainty'

The wait for Cabinet to announce its decision on whether schools will close or remain open amid the Covid-19 surge is causing more "anxiety and uncertainty", News24 reported earlier.

This is according to the country's two largest teachers' unions – the South African Democratic Teachers' Union (Sadtu) and the National Professional Teachers' Organisation of South Africa (Naptosa).

The two unions told News24 the wait was too long, causing unease among teachers and pupils.

Sadtu and Naptosa, along with other unions, met with Motshekga last week for a series of consultations to find a way forward for schools amid the peak in Covid-19 infections.

Following consultations with stakeholders, which also included School Governing Body organisations, Motshekga took their representations to the NCCC and subsequently Cabinet.

Sadtu general secretary Mugwena Maluleke said the unions were informed that Motshekga was still in meetings with Cabinet on Monday and Tuesday.

Infections on the rise

He said they had made it clear to the department that there was a sense of urgency, especially as infections were on the rise.

By Thursday morning, South Africa had recorded 572 new Covid-19-related deaths, the biggest spike in a single day, with most fatalities recorded in the Eastern Cape.



The cumulative number of deaths is now 5 940, Health Minister Zweli Mkhize said in a statement on Wednesday night.

The total number of confirmed infections in the country is now 394 948.

The number of recoveries currently stands at 229 175, which translates to a recovery rate of 58%.

The total number of tests conducted to date is 2 585 474.


  - Compiled by Riaan Grobler



Covid-19: More than 100 people must now be retested after samples lost in PE truck hijacking

  • A team of health workers has been dispatched to retest people whose samples were lost during a hijacking in Port Elizabeth.
  • The 111 samples, collected by a courier truck from seven clinics, were lost during the armed robbery in Motherwell.
  • The National Health Laboratory Services has condemned the incident.



Tracing and retesting of 111 people, whose Covid-19 samples were lost when criminals pounced on a courier truck during a heist in Port Elizabeth on Monday, is underway.

National Health Laboratory Service spokesperson Mzimasi Gcukumana said: "The NHLS have allocated healthcare workers to contact the patients and make arrangements to collect new samples."

The bio-hazard samples went missing on Monday when two workers, from a courier company hired by the NHLS to collect samples from local clinics, were ambushed by two gunmen.

The incident happened at 15:30 in Motherwell's NU 11 section. The truck was found abandoned 500m away with the samples missing. The courier drivers were also robbed at gunpoint of their cellphones.

The police are investigating a case of hijacking. The suspects remain at large, confirmed police spokesperson Colonel Priscila Naidu.

A police source close to the case said the 111 test samples were collected from seven clinics in the area. 

NHLS provincial manager Tabita Makula had revealed that the hijacking prevented the courier employees from collecting more samples at other clinics.

Gcukumana said: "NHLS condemns in the strongest terms the criminal act that occurred in Port Elizabeth, after one of the courier services' vehicles was hijacked while delivering the Covid-19 samples to the laboratory for testing.

"This shocking and appalling behaviour puts the lives of members of the public at risk and has a negative impact on the NHLS' efforts in assisting the government in the fight against the coronavirus disease in South Africa. The loss of the test samples places not only the patients and their families at risk, but it could also infect anyone who comes into contact with the stolen samples."

Highly infectious

These criminal incidents placed further pressure on already stretched resources, said Gcukumana.  

The laboratory services institute also warned the robbers and the public not to touch the samples, as they may be highly infectious.

The samples were stored in cooler boxes with ice packs to keep temperatures at cool levels.

The incident happened three weeks after a jogger found specimens dumped on the N2 roadside outside East London on 29 June.

The courier company involved in the earlier incident admitted that the 80 samples had fallen through the bakkie’s opened canvas cover. The company was later fired for negligence and risk to human life.

 Gcukumana said anyone who came across the missing samples should call the Port Elizabeth NHLS laboratory on 041 495 6158.

Naidu said: "The investigation is still underway, and no suspects have been found at the moment. We are following leads. We urge anyone who may have information that may lead to the arrest of the two suspects to please call the police or report to the nearest police station."


 Malibongwe Dayimani



Gautrain still plans 18 more stations - but money is tight due to Covid-19

  • The plans for an 149km expansion of the Gautrain are still awaiting approval from Treasury.
  • It said this week that “alternative funding options” are being considered.
  • The Gautrain Management Agency has proposed that vehicle licence fees and airport taxes as well as VAT be used for the project. 
  • For more stories, go to

The plans for an 149km expansion of the Gautrain, which will see it reach Soweto, Lanseria and Mamelodi eventually, are still awaiting approval from Treasury – which this week said “alternative funding options” are being considered.

The coronavirus crisis has wreaked havoc on government’s finances. Government is expecting to this year earn R300 billion less in tax than it had expected, while it has promised to spend R500 billion to help the economy and citizens amid the pandemic. Money is extremely tight, but the Gauteng Management Agent said this week it is still confident the project will continue.

According to the Gautrain Management Agency’s proposed plans, released last year, government would have to contribute around 30% of the multi-billion rand budget needed for the expansion. With the original Gautrain, the government provided almost 90%.

It is hoped that the private sector will contribute 33% with the next planned expansion. 

The rest may have to come from national levies such as vehicle licence fees and airport taxes as well as VAT – paid by people across South Africa, whether they use the high-end train system or not, the GMA proposes.

But government is already planning tax hikes of R40 billion in the next four years just to help prop up its finances following the coronavirus crisis. The first round of tax hikes will be announced in February.

Gautrain expansion

The first phase of the expansion – which is supposed to start in 2024 - will see the network expand by 32km from Marlboro to Little Falls in Roodepoort.  It will also consist of three new stations and an additional maintenance depot.


Phase 2 will see it expand into Soweto.  When the expansion is completed, the network will stretch into Boksburg, Lanseria, Irene and Mamelodi. 

The GMA says the expansion project is expected to create over 170 000 direct jobs, with Phase 1 being anticipated to secure over 30 000 jobs.

“Phase 1 has been submitted to National Treasury for Treasury Approval 1 (TA1) that will enable the commencement of the procurement phase of the project.  The GMA is awaiting feedback on the TA1 application from National Treasury.” 

For its part, Treasury this week said that “alternative funding options are being considered by the Gauteng Province working together with all stakeholders.”

Although the GMA anticipates that the project will commence “beyond the COVID-19 event”, the agency still has not named any contractors.

 “The announcements regarding preferred and successful bidders and associated costs will be made after the conclusion of the procurement phase which will follow the required approvals from National Treasury.

“TA1 approval will however enable the commencement of project preparatory work required to enable the said procurement. Any specialist advisory services that the GMA may require for the undertaking of this procurement will be sourced through the public procurement process,” said the GMA.

New fares from the expansion are part of national treasury consideration and will be confirmed after approval.

 Phumi Ramalepe , Business Insider SA



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