What was predicted has now come to pass. It is mid-winter and a Covid-19 storm surge is now sweeping across South Africa. On Wednesday Health Minister Zweli Mkhize reported that of the 45 389 Covid-19 tests processed 12 757 came back positive for the virus. On a seven-day rolling average confirmed cases are now over 12 000, up from 6 000 at the end of June, and reported deaths at 122, up from 60 in mid-June.

Testing, testing

Another indication of the severity of the epidemic currently is the percentage of tests coming back positive. This reached 5% in mid-May but has risen steadily since then, and was at 28% yesterday. This is indicative not just of a raging epidemic, but also of a lack of contact tracing, and under-testing. Once again, the National Health Laboratory Service has failed to perform.

The organisation promised in late March that “At the end of April, the NHLS will be able to process approximately 36 000 test in 24 hours.” It is currently processing about 15 000 tests per day, about the same number as it was processing a month ago. The positivity rate has more than tripled in that period. In the week ending the 4 July the NHLS also took over four days on average to process tests, compared to around two days in the private sector.

The provincial situation

If one analyses the national health department’s figures by province the epidemic clearly first hit the Western Cape, probably because it was seeded widely and early by visitors from overseas. On a rolling seven day average the province reached 100 confirmed Covid-19 cases on 26 April. The Eastern Cape followed on 16 May, Gauteng on 28 May and KwaZulu-Natal on 30 May.

Gauteng is now at the centre of the epidemic, with KwaZulu-Natal also seeing a dramatic surge in cases over the past few days. The daily confirmed case figures for the Western Cape though are not a reliable indicator of the trend in the province. The drop-off in mid-June was a product of the decision taken earlier that month by the provincial government to ration testing - due to a shortage and the backlogs that had resulted - to those “at highest risk and most vulnerable from dying”. The Western Cape government reported the results of just under 4 000 tests yesterday, fewer than in early June, of which a third came back positive.

If one uses reported Covid-19 related hospitalisations as the more reliable measure Gauteng nonetheless overtook the Western Cape at the end of June, and now has over three times as many patients in hospital with the disease.

Of the other provinces the North West reached 100 cases on a rolling seven-day average on 17 June, the Free State on 30 June, Mpumalanga on 3 July, Limpopo on 4 July and Northern Cape on 13 July. These confirmed case daily figures are indicative of trends, they are by no means capturing the full extent of the epidemic in the country, especially in medically under-serviced areas. The latter five provinces were generally testing less, but as of the week ending the 4^th of July the positivity rates were also generally lower, as seen from the following table released by the NICD.

Table 1: Weekly number of tests performed and positive tests, by province, South Africa, 14 June – 4 July 2020

The Western Cape

The ANC-governed Eastern Cape and the DA-governed Western Cape have approximately the same size population and provincial health budgets (R25bn in 2019/20). Recently the South African media has reported on the utter dysfunction of many Eastern Cape hospitals, and the horrors that have resulted. This story has now been picked up by the BBC’s Andrew Harding in a report and has travelled around the world.

By contrast, it appears that the Western Cape has managed the epidemic effectively thus far. The healthcare system has not been overwhelmed, treatment has been provided, and for whatever reasons the epidemic in the province has stabilised (at least for the moment). This is evidenced by the figures for hospitalisations, ICU admissions, and deaths.

 
Counter-intuitively, recorded Covid-19 related deaths seem to have peaked before hospitalisations. This may be a reporting issue, or it may be due to increasingly effectively treatment protocols being developed and implemented (the use of proning, high flow nasal oxygen and dexamethasone).

Deaths

The picture being provided by daily confirmed case numbers is clearly incomplete. However, it does appear as if the daily figures for Covid-19 related deaths released by Minister Mkhize are even more inadequate. These currently total 4 453. If critically ill patients die before being tested, or outside of hospital, and/or if there is an inadequate reporting system, then these will be underestimates. This currently seems to be the situation outside of the Western Cape. Gauteng, for instance, is only releasing figures for Covid-19 deaths erratically, and it is still reporting fewer deaths on a rolling 7-day average than the Western Cape is.

The South African Medical Research Council is tracking estimated excess deaths closely. In its most recent report it estimates that there were 10 994 excess deaths from natural causes between 6 May and 7 July 2020. At that point 3 502 Covid-19 related deaths had been confirmed by Mkhize. As can be seen from the table below “excess deaths” matched Covid-19 related deaths far more closely in the Western Cape than in the Eastern Cape, Gauteng, or KwaZulu Natal.

Table 2: Covid-19 related deaths reported vs. SAMRC estimates of excess natural mortality, up until 7 July 2020

As can be seen from the table below the trend nationally is sharply upwards. This is also the case in almost all provinces.

The Western Cape being the clear exception.