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COVID-19 and South Africa: The coming winter flood

An editorial on Politicsweb analyses the grim realities facing South Africa in the face of COVID-19 and concludes that it is unlikely that the state and private healthcare systems – which may well merge to battle the crisis – will be able to cope at the epidemic’s peak.

South Africa is in the initial phases of a COVID-19 epidemic, the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This novel coronavirus, which emerged in Wuhan, China in late 2019 is closely related to SARS-CoV-1, the disease that resulted in 8 098 cases, and claimed 774 lives in China, Taiwan and Hong Kong in the 2002 to 2003 period. As a new, highly infectious virus, humans lack immunity to it, and the production of a safe and efficacious vaccine is estimated to still be some 18 months away.

The first case in South Africa recorded by the National Institute for Communicable Diseases (NICD) was of a 38-year-old man who had travelled to Italy, along with his wife and nine other people. Since then the numbers have rapidly stacked up as travellers returning from overseas have been tested.

As of Thursday, 18th March, the NICD had conducted 3,026 tests, of which 116 had returned positive results. 102 of these were people who had been overseas, and 14 were cases of local transmission. Many of these were, presumably, close contacts of the returning travellers. Anban Pillay, the director general of the Health Department is quoted as saying that none of these people had to place any patient who tested positive in intensive, or critical care.

These figures tell you about the epidemic that is currently raging in Europe, but little about what is actually going on in South Africa. The great question is to what degree community spread is already occurring under the radar of the NICD surveillance system, and for how long. Testing has been generally been limited to those who presented with symptoms (which are similar to the flu) AND who had recently travelled to high risk areas, or who had been in contact with known cases (also in health care setting), or who presented with “severe pneumonia of unknown aetiology”.

It is only the last that is likely to detect community spread in the early phases of the epidemic, and it is a lagging indicator as the great majority of people, and especially the youth, only develop mild flu-like symptoms (if any). In other words, it is possible for the virus to infect hundreds of people before the first severe pneumonia case is reported. In Northern Italy, or Washington State in the US, it was only when the elderly started dying in numbers that those regions realised that they had an epidemic on their hands.

It is likely that people infected with the SARS-CoV-2 virus have been coming into South Africa from Europe since early February (if not China before that) and initiating trains of local transmission in a number of different areas. In Australia, over 80,000 tests have been conducted and as of 19th March 2020 and 565 cases confirmed. Of these 259, or under half, were considered to be overseas acquired.

The real signal to look out for then is not the number of people returning from overseas with COVID-19, and their close contacts, but the first cases of acute pneumonia caused by SARS-CoV-2 in old age homes or informal settlement areas like Diepsloot and in Khayelitsha. The spread, and the severity of symptoms, may have been suppressed by the warm summer weather in the southern hemisphere. Last year the influenza season began in late April in South Africa, so any respite still being provided by our converse seasonality to the northern hemisphere will be potentially short lived.

To understand the likely course of the COVID-19 epidemic over the next six months it is useful to examine how it has affected societies elsewhere, and then compare them to our own.

Unlike in Europe and the US, China and South Korea currently have their epidemics largely under control partly through aggressive testing and contact tracing. This means that they have a fairly comprehensive picture of who has been infected by SARS-CoV-2, including those who displayed only mild symptoms. As can be seen from Tables 1 and 2 while the young can be infected, and be carriers of the virus, those under thirty were highly unlikely to die from the disease. While those under 50 accounted for 58,6% of all confirmed cases in South Korea, there have been only two deaths among under-50s so far. As you get older the fatality rate becomes higher, increasing dramatically for those over sixty.

Table 1: Confirmed cases and deaths in South Korea as of 17 March 2020

Age-group Confirmed cases % of all cases Deaths % of all deaths Fatality rate
0 to 9 86 1,0% 0 0,0% 0,0%
10 to 19 436 5,2% 0 0,0% 0,0%
20 to 29 2 330 28,0% 0 0,0% 0,0%
30 to 39 856 10,3% 1 1,2% 0,1%
40 to 49 1 164 14,0% 1 1,2% 0,1%
50 to 59 1 602 19,3% 6 7,4% 0,4%
60 to 69 1 033 12,4% 16 19,8% 1,5%
70 to 79 539 6,5% 29 35,8% 5,4%
80+ 274 3,3% 28 34,6% 10,2%
  8 320 100,0% 81 100,0%  


Table 2: Confirmed cases and deaths in China between 1st January and 11th February 2020:

Age-group (years) Confirmed cases % of all cases Deaths % of all deaths Fatality rate
0 to 9 416 0,9% 0 0,0% 0,0%
10 to 19 549 1,2% 1 0,1% 0,2%
20 to 29 3 619 8,1% 7 0,7% 0,2%
30 to 39 7 600 17,0% 18 1,8% 0,2%
40 to 49 8 571 19,2% 38 3,7% 0,4%
50 to 59 10 008 22,4% 130 12,7% 1,3%
60 to 69 8 583 19,2% 309 30,2% 3,6%
70 to 79 3 918 8,8% 312 30,5% 8,0%
80+ 1 408 3,2% 208 20,3% 14,8%
  44 672 100,0% 1023 100,0% 2,3%

If the health system is overwhelmed in a country, and is unable to provide proper care to most patients with acute pneumonia, then the survival rate of those needing hospitalisation will drop precipitously.

One of the advantages South Africa has, relative to East Asian and European countries, is the young age of the population. 59,1% of the South African population is under 30 years of age. 87,6% under the age of 50.

Table 3: Age profile of the South African population by numbers

Age-group Black African Coloured Indian/Asian White RSA
0 to 9 9 838 467 952 930 195 951 484 037 11 471 385
10 to 19 8 542 208 860 253 179 296 506 148 10 087 904
20 to 29 8 812 127 864 308 234 687 531 635 10 442 757
30 to 39 8 428 586 791 846 281 140 607 565 10 109 138
40 to 49 5 113 227 627 611 224 610 665 577 6 631 025
50 to 59 3 353 082 554 459 176 177 643 842 4 727 560
60 to 69 2 112 537 340 095 124 241 577 724 3 154 597
70 to 79 920 609 142 276 65 298 419 504 1 547 687
80+ 322 416 42 971 21 608 215 973 602 969
Total 47 443 259 5 176 750 1 503 007 4 652 006 58 775 022


Table 4: Age profile of the South African population by proportion

Age-group (years) Black African Coloured Indian/Asian White RSA
0 to 9 20,7% 2,0% 0,4% 1,0% 24,2%
10 to 19 18,0% 16,6% 11,9% 10,9% 17,2%
20 to 29 18,6% 16,7% 15,6% 11,4% 17,8%
30 to 39 17,8% 15,3% 18,7% 13,1% 17,2%
40 to 49 10,8% 12,1% 14,9% 14,3% 11,3%
50 to 59 7,1% 10,7% 11,7% 13,8% 8,0%
60 to 69 4,5% 6,6% 8,3% 12,4% 5,4%
70 to 79 1,9% 2,7% 4,3% 9,0% 2,6%
80+ 0,7% 0,8% 1,4% 4,6% 1,0%
Total 100,0% 100,0% 100,0% 100,0% 100,0%

Only 6% (3,5m) of the population is over the age of 65. This compares to Italy, which has a similar size population, where over-65’s make up 23% (14m) of the total population. Advice published by Harvard University said: “People who are older and older people with chronic medical conditions, especially cardiovascular disease, high blood pressure, diabetes, and lung disease are more likely to have severe disease or death from COVID-19, and should engage in strict social distancing without delay. This is also the case for people or who are immunocompromised because of a condition or treatment that weakens their immune response.”

The most critical unknown about the looming COVID-19 epidemic in South Africa is how the disease will intersect with the massive number of TB and HIV/Aids cases in the country. As the Academy of Sciences of South Africa recently noted, “it is not known whether individuals with Human Immunodeficiency Virus (HIV) or underlying tuberculosis (TB), both of which are highly prevalent in South Africa, are at increased risk for severe disease following infection with SARS-CoV-2. This is especially relevant based on evidence that individuals living with HIV have an eight-fold greater burden of hospitalisation for pneumonia due to influenza virus, and a three-fold higher case fatality risk.”

According to World Health Organisation estimates the incidence (number of new cases) of TB in South Africa was around 301 000 in 2018, with HIV-positive TB incidence at around 177 000. In 2016 StatsSA estimated that TB (of either type) was the leading cause of death among South Africans. 29,399 of the 454 989 deaths recorded that year were attributed to this disease. The WHO though put the estimated number of deaths from TB at 63 000 in 2018.

The South African National HIV Prevalence, Incidence, Behaviour and Communication Survey, 2017 estimated that there were 7,9m South Africans living with HIV that year. Of these 4.4m were on anti-retroviral treatment (ART), and 3.5m not on treatment. Of those with HIV an estimated 4,9m had suppressed viral loads – a sign of effective treatment and/or immune response – while 1.6m did not.

HIV cases in South Africa in 2017 by age and treatment status.

Age group (years)  HIV positive On ART Not on ART Viral load suppressed Viral load not suppressed
0–14 451 570 131 000 320 570 234 365 63 011
15–24 760 238 274 000 486 238 360 353 144 124
25–49 5 595 638 3 244 000 2 351 638 3 514 060 1 206 768
50 and older 1 122 282 753 000 369 282 821 510 201 804
Total 7 929 728 4 402 000 3 527 728 4 930 289 1 615 707


The probable situation now is that the SARS-CoV-2 is already present, and quietly spreading, in many different communities in South Africa. The symptoms being presented are mild, to non-existent, as the NICD has yet to start picking up on severe cases. To the extent that warm weather has provided a break on its spread and severity, this will be lifted once the first winter cold front sweeps across the country.

While government measures announced by President Cyril Ramaphosa have concentrated the minds of South Africans, it is doubtful for how long the epidemic can be contained. For example, if one begins with 100 undetected internal cases, and the number doubles every three days (currently the rate of increase in some European countries), you will go from 100 cases to 100,000 in 30 days.

It is true that Singapore, Taiwan, Hong Kong and South Korea all managed to keep a lid on the epidemic in their countries. But these are all nations with highly effective states and disciplined societies which experienced, and learnt lessons from, the first SARS epidemic in 2002 and 2003. They reacted very quickly and effectively to this new, but familiar, coronavirus.

They have combined social distancing with the ubiquitous wearing of masks in public, the testing of all those with symptoms, the quarantining of those who test positive, and highly aggressive and effective contact tracing. They are also all (in effect) island nations, able to now restrict entry across their borders, and thereby minimise the re-importation of the virus from overseas. Europe, the UK and the US are stumbling far behind, still not knowing quite what to do.

South Africa lacks the masks, the tests, and the necessary state capacity, and will do so through the course of the epidemic. If one region of the country were to halt the spread of the virus temporarily, it could be re-imported from any other. The living and transportation conditions of millions are crowded and awful. There are also 10m twenty-something South Africans. This is an age cohort that is highly social, and notoriously irresponsible. Unless there is some as yet unknown obstacle in the path of the virus – not present in Europe or Asia – it is likely to spread rapidly across the country. Beyond a certain point testing, contract tracing and quarantining people will become futile and redundant.

The best response to the coming winter flood is not to invest everything in trying to stop it, which may well ultimately prove impossible, but to (also) try and ensure that as many among the most vulnerable in society are on safer, higher ground. This includes medical workers, the elderly, those with pre-existing medical conditions, including those with TB, and those with immune deficiency.

Doctors and nurses need access to proper protective equipment. Old age homes need to develop strict protocols to keep out the virus. Elderly people and those with pre-existing medical conditions need to self-isolate. Employers should do whatever is necessary to minimise the chances that vulnerable employees – such as those being treated for TB (or with lungs damaged by TB) – become infected over the winter. If it is not already too late to do so the state should seriously encourage people to get tested for HIV and go onto ART.

It seems unlikely that the state and private healthcare systems – which may well merge to battle the crisis – will be able to cope at the epidemic’s peak. The Wits health economist Alex van den Heever has estimated that there were approximately 4,960 critical care beds in the private sector in 2017, with 60% availability, and approximately 2,240 critical care beds in the state sector, with 20% availability. This would mean that around 4,000 such beds are currently available for severe cases of COVID-19. Once the first person has to be hospitalised, and assuming the number of those so afflicted doubles every 2.3 days, then all those beds would be occupied within the space of a month. No-one can be confident then that there will be a critical care bed available for them should they develop severe illness over the winter.

In such situations it is worth returning to the parable of the Sultan’s horse.

Two condemned prisoners were brought before the Sultan in fetters, one after another, to hear their fate. The Sultan addressed them, each in turn, as follows: “I am sentencing you to death by decapitation. However, I am willing to offer you a reprieve if you will teach my favourite horse to talk.”

The first prisoner indignantly replied: “What kind of choice is this? That is impossible!” “So be it”, replied the Sultan, and the man was dragged outside by the guards, to await his imminent execution.

A short while later he saw the second prisoner walk out of the room, a free man. Perplexed, the first prisoner asked him: “What did you tell the Sultan?”

The second man replied, “I said that I could certainly teach the horse to speak, but that it is an exceedingly difficult and time-consuming task, and it will take a year. He then said I could go free, but if I fail in my task I will be beheaded.”

The first prisoner exclaimed: “well, then you are most certainly doomed! No man has ever achieved that!” To which the second man replied: “That is true. But a lot can happen in the year. Perhaps I will die peacefully in my sleep. Perhaps it is the Sultan himself who will die. Or perhaps even – who knows! – I will be the first to get such an animal to talk!”

South Africans, along with others around the world, are currently in the position of the two prisoners. There is neither a vaccine for SARS-CoV-2, nor a treatment for COVID-19. Humans lack immunity to it, and it is estimated that over half the world’s population will eventually contract it. For many of those over 60 it is a death sentence should they become infected.

The measures needed to temporarily check its spread cause acute economic and social distress.

Yet a lot is likely to happen over the next six months. Treatments will be developed and refined by researchers around the world. Progress will be made towards a vaccine. The understanding of the disease, how it is transmitted, and how to limit its spread, will rapidly develop.

If the epidemic runs largely unchecked in South Africa through winter the great majority of younger and healthy people will get the virus, develop only mild symptoms, and recover. They will thereby attain a degree of immunity which will, in aggregate, provide herd immunity to the broader society. This has the potential to bring a sustainable end to the epidemic in South Africa.

The important thing over the next six months is to do whatever it takes to protect yourself, if you are at high risk, and to protect and support others if you are not.

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