Microbes, mobility and mortality: South Africa’s long pandemic history

By Emeritus Professor Howard Phillips

Pandemics are spread by people moving around. The lesson from this is that the way to curb the spread of the coronavirus in South Africa is to maintain tight control over the movement of individuals. This is a lesson we have always found hard to follow, but have had a long time to learn. On several occasions since the arrival of Dutch settlers to the Cape different infectious diseases have taken hold of the indigenous population and since the 18th century they have clearly mapped out the dominant pathways of human movement to and within the sub-continent.

 South Africa is no stranger to pandemics. The region’s history reveals that it has on several occasions been overtaken by a pandemic, that is, an infectious disease caused by a pathogenic microbe sweeping the globe, which has struck down or even killed an unusually large number of its inhabitants. It is on how the worst of these spread to and within South Africa that this article will focus, in a bid to put one important aspect of the current Covid-19 pandemic into historical perspective.

Apart from the possibility of an epidemic (an excessive local or regional outbreak of a disease) having hit Mapungubwe in the Limpopo Valley early in the second millennium AD,[1] there is at present no strong evidence of such episodes in South Africa before the 17th century. Indeed, in 1678 a group of Khoekhoe leaders told the Dutch authorities at the Cape that ‘no particular severe sicknesses are known among them, and Death usually contents himself with old worn out people’.[2] But even as they spoke these words, the disease environment in which they and their forebears had lived for millennia was being fundamentally altered by the region’s burgeoning connections with Europe and Asia, which the Dutch East India Company’s colonial settlement at Table Bay had formally inaugurated in 1652.

As had happened with the Spanish arrival in Latin America 150 years earlier, this Dutch presence and the interaction with the indigenous population which it brought once and for all breached the isolation which had hitherto shielded locals from the infectious disease pools of Europe, the Middle East and Asia. ‘Great sickness’ began to be reported more and more frequently among the Khoekhoen. In 1687, for instance, Dutch officials recorded that in the southern Cape, ‘there is a very severe and deadly sickness among the Hottentots [sic] who do not know what to do for it; and although they decamp and move from place to place, the sickness still pursues them …. The burning fever drags many, both old and young to their graves.’ That earlier in that month an ‘infectious fever’ had been raging in Cape Town, causing many deaths, strongly suggests the source from which that disease had reached the southern Cape.

Whatever this lethal disease was, it proved but an ominous forerunner to the first identifiable pandemic which struck the sub-continent with devastating effect in 1713, smallpox. Part of an ongoing pandemic which swept the world repeatedly from the 16th century onwards, after 1713 it returned at least a dozen times to the sub-continent over the next 180 years. Thrice during the Dutch East India Company period it was introduced by sailors and passengers aboard Company vessels travelling to Europe from Dutch colonies in the East Indies. In each case it was their smallpox-infected clothing which transmitted the causative variola virus to the unprotected population of the Cape, via laundrywomen in 1713 and 1767 and via second-hand clothes dealers in 1755. From Cape Town it was carried inland by infected individuals fleeing the disease.

In the 19th century, as the Cape’s connection to the international trading system changed as a result of it becoming a British colony in 1806, so did the source but not the fact of its further smallpox epidemics alter. Thus, in 1812 and again in 1840 it arrived aboard a Portuguese slave ship brought into Table Bay after being captured off Mocambique by the Royal Navy’s Anti-Slavery Squadron, while the 1882 epidemic reached Cape Town aboard a steamship straight from Britain. As in the 18th century, smallpox was also transmitted from the coast into the interior by infected people travelling there. Smallpox ‘always comes from the south’, an explorer was told in 1860 by Ngwato tribesmen near Lake Ngami in today’s Botswana.[3] Where it travelled, a local told him, ‘there are no people left, only stones’.[4] Thus, like a chemical marker used to track digestion, the smallpox epidemics of the 18th and 19th centuries clearly map the dominant pathways of human movement to and within the sub-continent.

Smallpox was already receding as a serious threat to health in the sub-continent thanks to the introduction of vaccinations when a second pandemic reached South Africa in 1900, bubonic plague, which had begun to spread from China to ports around the world in 1894. Travelling also by sea, but in this case not in humans but in fleas on rats aboard ships, the causative bacillus, Yersinia pestis, arrived in Cape Town from Argentina with cargoes of fodder to feed the horses of the British army involved in the South African War. From September 1900 numbers of dead rats began to be noticed in the section of Cape Town’s harbour reserved for military use. An officer reported seeing sick rats ‘coming out to the open daylight, in a dazed state so that you could catch them with your hand.’[5] However, the local military command did not share news of this rodent die-off with the municipal health authorities, and so it was not until fleas carrying the bacillus turned from dead rats to living human beings nearby, and civilians working in the harbour began to die, that the outbreak of bubonic plague in Cape Town was officially acknowledged.

From Cape Town and the other South African ports similarly infected bubonic plague did not spread far inland, except in one significant case, when a man with the pneumonic variety of plague (which is readily transmissible from person-to-person) travelled from East London to Johannesburg where he infected his family and their neighbours, triggering a short, sharp pneumonic plague epidemic in that town.

Military priorities were also responsible for the introduction and primary spread of the devastating Spanish flu pandemic 18 years later, in 1918. Two troopships carrying South African Native Labour Corps soldiers home from Europe during World War I arrived in Table Bay in September of that year. Both had cases of influenza on board after having stopped on the way at Freetown, Sierra Leone to take on coal. Even though influenza had been raging in Freetown at the time, interaction between the two ships and the dock colliers had not been restricted as the port authorities hesitated to interfere in naval matters. The consequences of this contact became apparent on the next leg of voyage to Table Bay, when influenza began to occur onboard both vessels, prompting Cape Town’s port health officer to propose that all aboard be quarantined when the vessels arrived there. However, at the behest of the military authorities, the port health officer recalled in his own defence, he was overruled “as the men were away from home so long, it would be unfair to keep them under quarantine for so long in Table Bay harbour. He must allow them to land and go home.”[6] As a compromise, only those who were still sick were hospitalised on shore, while the rest were confined to a military camp where they were placed under cursory quarantine, tested and, after two days, officially demobilised and allowed to entrain for their homes across the sub-continent.

No sooner had they left the city than cases of severe influenza akin to the so-called ‘Spanish’ flu in Europe and Sierra Leone began to appear in Cape Town among stevedores and dock labourers, fishermen and the military staff at the hospital and camp where the newly-arrived soldiers had been lodged. By then, however, the troops themselves were disembarking at stations along the country’s extensive railway network, many of them now infectious and thus transmitting the Spanish flu virus to their families and the communities which had proudly gathered to hail their safe return from the Great War. From as remote a district as Tsolo in the Transkei, for example, a magistrate reported that, since the return of a batch of Native Labour Corps troops early in October, “sickness has become rife amongst both races in village and country and people are being brought in to [the] local doctor by wagon and sledge loads”.[7]

Yet, returned soldiers were not the only vectors of Spanish flu. Their transmission of the disease countrywide was supplemented by other effective vectors, viz. families fleeing infected towns for their lives, railway personnel travelling between stations and, particularly, migrant workers desperate to escape from mine compounds and barracks where death was rampant. In Kimberley, for example, thousands of diamond miners insisted “that if they had to die they would rather die at home and that they also wished to go and look after their families”. A week later they “had made up their minds to leave,” reported a panicky labour agent, “and [declared that] if De Beers [the mines’ owner] did not agree they would break out, even if fired upon”.[8] In many cases the conditions under which they and other migrant workers returned home were grim. It was reported from Pietersburg, for instance, that corpses of mineworkers were being “found alongside the railway track all the way to Messina”,[9] while a farmer in the Graskop district came across “natives [sic] all along the road just left to die.”[10] Paradoxically, many of those who struggled so to reach their family homes brought the flu virus with them and thereby the risk of infecting their very own households. Graphic and telling in this regard is an account by a man who had been a migrant worker on the diamond mines in Kimberley in 1918 before leaving for his home in the Taung district at the end of his contract: “He caught the 8 p.m. train to Mafeking. On the journey, passengers were taken ill and some died. He got off with one of his friends at Jan Kempdorp (Border station) and they began to walk home. As they walked, he began to shiver … and soon he and his friend could only crawl, unable to carry their luggage. He struggled on in this way on his knees for the whole day. He reached his home at Driefontein on 3 October and fell into a deep sleep. He only regained full consciousness on 19 October. During those 16 days he was delirious, imagining that he saw his friends when in fact they had died. He believed that ‘I carried the “fever” [Spanish flu] to Driefontein.”[11]

It is likely that returned soldiers were also the vectors who introduced a new strain of yet another pandemic, polio, to South Africa from the Middle East towards the end of World War I in 1917, and towards the end of World War II in 1944. On both occasions, no sooner had these troops disembarked in Durban than serious cases of this disease began to appear in local battalions and among the staff of military hospitals where they were being treated. From these military hotspots it spread to civilian communities, unchecked by a government unwilling to single out its soldiers as being primarily responsible. This reconstruction of the pathway of the polio pandemic into South Africa is supported by the fact of similar outbreaks at the same time in the USA, Britain, New Zealand and Australia to which their own troops had recently been repatriated, also from the Middle East. Two further outbreaks, in 1947 and 1956, were not obviously linked to the military, but identifying their source was overshadowed by vigorous campaigns in these years to raise funds for medical research to develop a preventive vaccine, a goal which achieved spectacular success in the mid 1950s. Thereby polio was eliminated as a threat to the population of the country.

In the case of the next pandemic to hit South Africa, HIV/AIDS, finding a preventive vaccine is still work in progress today, but medical research has at least rendered it treatable, turning it into a chronic disease which can be managed.

Its path into and within South Africa was along two very different migrant worker routes. The Clade B subtype was probably introduced in the late 1970s by aircrews returning home from the USA where it had begun to manifest itself among gay men. Two SAA stewards who died in Pretoria in 1982 of a pneumonia that their deficient immune systems could not fight off were the first cases to be recorded in the country. Within a year 32 more gay men in Johannesburg were diagnosed as HIV+.

The second HIV subtype, Clade C, seems to have arrived in South Africa a little later via quite different vectors, migrant labourers coming to work on the Witwatersrand gold mines from Central Africa which was adjacent to the then epicentres of the pandemic, Uganda and Zaïre. The first recorded cases of this clade were diagnosed among migrant Malawian miners on the Rand in 1986. Within two months, two local women who had consorted with these miners were diagnosed as HIV+ too. From these sources HIV slowly began to be seeded among other miners and workers on the Rand and then among their families and communities when they returned to their rural homes at the end of their contracts or during Christmas vacations. By 1992 at least 2.2% of pregnant women attending public sector health facilities in South Africa were HIV+.

As vectors of the disease migrant workers were soon joined by other categories of young people on the move: long-distance truck-drivers whose number and routes grew markedly from the 1980s as restrictions on road freight transport were eased and who were known to frequent sex-stopovers along the many domestic and foreign roads they traversed; young political exiles returning home from East and Central Africa after 1990 as South Africa entered its transition to democracy; and, after the advent of democracy in 1994, foreign refugees and asylum-seekers from elsewhere in Africa. By 1995 10.4% of pregnant women being tested at state health facilities were HIV+. Five years later this figure stood at 24.5%.

Sailors, soldiers, ship and train passengers, migrant workers, truckers, exiles, refugees and asylum-seekers – what do these, the principal vectors of pandemics to and in South Africa over the last 300 years, have in common? The answer is physical mobility, for it has been human mobility by sea, road and railway which has unwittingly brought global pandemics to South Africa and then spread them within the country.

The underlying reasons for this are fourfold: South Africa’s geographical position on an increasingly busy sea-route between Europe and Asia and its pivotal place, as a consequence, in the burgeoning modern world trading system; the military priorities of successive rulers of the region outweighing public health precautions; the nature of South Africa’s industrial system, with its heavy reliance on migrant labourers who travelled along its extensive rail and road networks between their places of residence and of work; and its two national political systems before and after 1994, the first of which saw a significant number of its people take refuge in neighbouring countries to escape apartheid and the second of which opened a democratic South Africa to returning exiles and refugees. In short, people on the move have been the means by which pandemics have been introduced into the country and then spread there.

Nor, as the current Covid-19 pandemic makes clear, does this feature belong only in the past. In 2020, in a world of swift, easy travel between continents by air, Covid-19 appears to have been introduced to South Africa by infected South African tourists returning home on flights from a Covid-19-struck Europe and North America and by infected European tourists visiting the country. Through their contacts with South Africans the coronavirus was then transmitted to locals who, in turn, spread it within their immediate urban communities and even into rural areas to which they travelled by road and train to seek refuge or to bury family members who had succumbed to the virus. As this article shows, this is a pattern of human mobility which parallels closely the region’s long epidemic history. A resident who tried to keep Covid-19 out of his home village of Genadendal by blocking the entrance road understood this fact all too well, telling a journalist recently, ‘We saw that the moment we can stop the movement of the people, that’s the moment we can stop the movement of the virus.’[12]


Emeritus Professor Howard Phillips was on the staff of the Department of History at UCT where he taught, amongst others, medical history and the history of epidemics. He is the author and editor of numerous works on the Spanish flu pandemic and has written innovative histories of Groote Schuur Hospital and the University of Cape Town. His most recent book is UCT Under Apartheid: Part 1 – From onset to sit-in, 1948­–1968 (Jacana Media) https://jacana.co.za/our-books/uct-under-apartheid-from-onset-to-sit-in-1948-1968/



[1] S. Chirikure, ‘Archaeology shows how ancient African societies managed pandemics’ in The Conversation, 14 May 2020 at https://theconversation.com/archaeology-shows-how-ancient-african-societies-managed-pandemics-138217

[2] Cited in H. Phillips, Plague, Pox and Pandemics: A Jacana Pocket History of Epidemics in South Africa (Jacana Media), p. 14.

[3] Cited in Phillips, Plague, Pox and Pandemics, p. 29.

[4] Cited ibid. p. 37.

[5] Cited ibid. p. 43.

[6] Letter to author from Dr J.P. Immelman, 29 May 1978. Dr Immelman was a friend of the said port health officer, Dr Keet.

[7] Cited in H. Phillips (ed), In a Time of Plague: Memories of the Spanish Flu Epidemic of 1918 in South Africa (VRS, Cape Town, 2018), p. xii.

[8] Cited ibid. pp. xii-xiii.

[9] Cited ibid. p. xiii.

[10] Cited ibid. p. xiii.

[11] Cited ibid. p. 94.

[12] Mail & Guardian, 26 June 2020.

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