Ending the lockdown – The big problem with South Africa’s coronavirus statistics

It is not currently possible to compare South Africa’s coronavirus statistics from last week to the week before. This is according to Health Minister Zweli Mkhize and his advisor Salim Abdool Karim.

Karim is an epidemiologist who chairs the Minister’s COVID-19 advisory group.

During a recent [email protected] event hosted by UKZN, Karim explained that due to changes in the way data is reported, it is not possible to simply compare coronavirus case numbers from this past week to the week before.

This is because until recently, all of the coronavirus cases identified in South Africa came from passive reporting. This is when someone starts to feel ill and goes to a doctor, clinic, or hospital.

Over a week ago, the Department of Health embarked on a large-scale active screening campaign. Around 28,000 community healthcare workers have been deployed to vulnerable communities where they are screening people for potential infections.

When the screening process identifies someone as possibly having an infection, they are referred to a laboratory or clinic for a SARS-CoV-2 test (also referred to as a coronavirus test).

Karim initially said that community healthcare workers had screened a million people in 6-7 days, and had referred 10,000 for a test.

Minister Mkhize later corrected those figures to around 900,000 people screened, with 11,000 referred for testing.

According to Karim, the goal is to screen about a million people per week.

Extending the lockdown – the decision tree

These figures are important, as they are the key metric the Department of Health provided for deciding whether to extend or relax the lockdown.

The government was watching the number of new cases reported as a result of passive screening from 10-16 April. By 18 April, Karim said they would be able to make a decision on whether to extend or relax the lockdown.

Unfortunately, this turned out to be more difficult than first thought, and no decision has been communicated regarding lockdown.

Apples and oranges

While the active community screenings have dramatically improved the level of coronavirus testing in South Africa, they have made it difficult to conduct a week-to-week comparison of the number of new coronavirus cases.

“If you compare the numbers from this week with last week, you are not comparing apples and apples. We are, in effect, comparing apples in [one week], with apples and oranges in the [following week],” Karim said.

He explained they need a way to “tease out” the number of positive coronavirus cases that were identified due to active screening.

However, they don’t currently have a tool that can filter active and passive results.

“We’re trying our best right now,” Karim said. “I’m trying to make some estimates.”

He also took responsibility for setting the lockdown extension criteria without properly taking into account the challenges in analysing data from passive and active case finding.

“When you look at data, you have to understand its source, you have to understand its comparability. I didn’t factor that into my thinking,” he said.

He also stated there are ways in which they can deal with passive and active tests results being mixed together.

“None of this is a complete train smash. We’re smart people, we can figure this out,” he said.

“One of the ways is to use a stratified analysis. If you stratify your data you get rid of the mixing effect, you get rid of the confounding,” stated Karim.

“That’s one of the strategies we have available to us. How we use it, whether we use it, I am not sure yet. We will know in a bit.”

Total confirmed cases

The chart below shows the total number of positive coronavirus cases identified in South Africa since 5 March.

There is a clear change in the slope of the graph from 12 April, showing an increase in the number of new coronavirus cases as the number of tests increased.

Big rise in new coronavirus cases

The following chart plots the daily number of new coronavirus cases in South Africa against the number of new tests conducted.

It shows that higher daily case numbers tend to coincide with days where there was a high number of new test results reported.

Week-to-week comparison

The following chart compares the average number of new cases per day, over a week, to the average number of new test results being reported per day.

These averages are calculated from Friday to Thursday, so that the start of a given 7-day period coincides with 27 March 2020 – the day that South Africa entered its lockdown.

Not depicted in this chart is the dramatic increase in the number of new cases and test results since 17 April.

On 17 April, there were 178 new cases and 5,767 test results reported. The next day there were 251 new cases – the highest number to-date – along with 7,194 test results.

Yesterday there were 124 new cases and 6,690 test results.

This week is therefore on track to have the highest number of new coronavirus cases per day since the beginning of the outbreak, along with the highest number of test results reported.

Rise in new cases and a lockdown extension

Mkhize has also stated that a rise in new COVID-19 cases does not mean the lockdown will be extended.

Taking active screening and testing into account, Mkhize said the COVID-19 advisory group felt there was not a “huge indication” of a big increase in new cases at this stage.

Mkhize further highlighted that Karim’s infection criteria are not the only considerations when deciding on extending the lockdown.

He said they are also looking at the economic impact of the lockdown, people going hungry, and creating a sustainable environment to curb the spread of the virus.

He said the government wants to contain the spread of COVID-19 in a way which will also allow people to work, earn a salary, and have enough food to eat.

After the lockdown won’t be business as usual

While the lockdown may not be extended beyond 30 April, government officials have made it clear that it also won’t be lifted immediately.

Minister of Cooperative Governance and Traditional Affairs Nkosazana Dlamini-Zuma said that should the lockdown not be extended beyond 30 April, it also won’t suddenly end.

“We can’t open the floodgates,” she said.

Her statements echo earlier remarks from Karim, who said that certain limitations will remain in effect even after the official lockdown ends.

Dlamini-Zuma also stated that certain restrictions are likely to remain in force “for a very long time”.

She said the current restrictions will be adapted on a weekly basis. These changes will include industry sectors being allowed to operate again as the restrictions are gradually eased.

Karim said that in addition to certain limitations remaining in place, such as those on travel and large gatherings, there will also be a programme of constant coronavirus surveillance to ensure the spread of the virus is kept in check.

Specifically, this will include a regular national surveillance day for schools, mines, prisons, and big companies to screen people for the coronavirus. This will happen one day per month, or more regularly.

The government wants to use 5% of staff from emergency rooms, ICUs, and respiratory units to be part of this national surveillance programme.

Now read: Behind the scenes at South Africa’s impressive COVID-19 tech hub

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Ending the lockdown – The big problem with South Africa’s coronavirus statistics