South Africa passed another grim Covid-19 milestone on Monday, as it surpassed the 100,000 mark for confirmed infections. This is less than three months since the first recorded death.

There were also a further 61 Covid-19 related deaths in the past 24 hours, bringing the total deaths to 1,991.

However, according to Prof Salim Abdool Karim, a leading clinical infectious diseases epidemiologist and government adviser, this was “more or less” where experts predicted it would be in its fight against the pandemic.

SA recorded its first confirmed case on March 5, when a 38-year-old male who travelled to Italy with his wife tested positive. Less than a month later, on March 27, two deaths were reported - the first fatalities from the respiratory illness.

Since then, with the Western Cape as the epicentre, SA had recorded 1,991 deaths and 101,590 confirmed cases of the illness, health minister Dr Zweli Mkhize said on Monday night.

The climb to 100,000 cases has been dramatic.

On June 1, SA had 34,357 cases. By Sunday, just three weeks later, this had increased to 97,302 cases - and then increased by 4,289 cases to the 101,590 announced by Mkhize on Monday night.

The last time fewer than 2,000 new cases were reported over a 24-hour period was on June 3, and the last time fewer than 1,000 cases were reported in a single 24-hour period was on May 26.

In fact, just once in the last 10 days has SA had fewer than 3,000 new cases. That was on June 16, when 2,801 new cases were announced.

The three days with the biggest number of new infections were:

• June 20 - 4,966 new cases; followed by
• June 21 - 4,621 cases; and
• June 14 - 4,302 cases.

The deadliest days were:

• June 19 - 94 deaths;
• June 15 - 88 deaths; and
• June 8 and 9 - 82 deaths each.

However, Abdool Karim said the situation in SA was as expected.

“As the epidemic looks right now, we are more or less where we anticipated we would be at this time of the epidemic,” he said in an interview with TimesLIVE.

Abdool Karim said when the government implemented lockdown regulations on March 26, they were able to slow the spread of the virus "substantially" - but this has changed as the country has moved to lower levels.

“As we reached the tail-end of the level 5 restrictions, we started seeing some small outbreaks in the supermarkets [and] grocery stores in the Western Cape,” he said 

“By the time we got into level 4 restrictions, the epidemic was already starting to grow in the broader Cape Town area. We began to see quite substantial increases at the tail-end of level 4 restrictions and that has just continued to grow under level 3.”

As the Western Cape remains the epicentre of the virus with 52,554 of the total infections and 1,458 of the deaths by Monday night, Abdool Karim said the province had reached a “fully fledged” epidemic.

The Eastern Cape remains second-worst in terms of deaths (303) and third in terms of cases (16,895). Commenting on the Eastern Cape figures,Abdool Karim said they were a result of the linkages between it and the neighbouring Western Cape, but the province nonetheless remained at the early stages of its likely Covid-19 trajectory.

“We are also seeing some of the cases in the Eastern Cape were actually imported from the Western Cape, but the Eastern Cape also has its own local transmissions that occurred through funerals, prison warders, communities. It spread rapidly, but the province is still at early stages.” 

Gauteng 'better than expected'

Abdool Karim praised Gauteng, which is second with 22,341 cases and 122 deaths by Monday night, for doing well in flattening the curve and slowing the infection spread.

“When we were looking at projections in March, I would not have guessed that the epidemic would grow first in the Western Cape. All data we had suggested it would grow most in Gauteng, because of its density and large populations, we thought it would grow fastest there,” he said.

“I don’t fully understand why it didn’t grow as fast in Gauteng, especially given that there is an international airport, and there a lot of international travellers. But it looks like some of the steps that were taken were quite effective in terms of reaching out, doing contact tracing, putting up quarantine sites.”

However, he warned that the province was not in the clear. “It has never eliminated the problem, and it’s never been contained. There has been ongoing transmissions.”

Abdool Karim said the worst was still to come for SA. “From an epidemiological basis, we can expect that we will have a few hundred thousand cases by the end of July, and that’s just based on the current doubling time that we would expect that sort of situation to occur.

“We all know the worst is yet to come. All we can do is continue our preparation and hope what we’ve done will be enough to mitigate what’s to come. This virus is here to stay for a little while - it’s not going anywhere.”

Karim pointed to China, which had bought the virus under control. However, there have been recent cases - including a spike of infections last week in Beijing, which has since gone under lockdown. The same thing happened in South Korea, which was also one of the countries impacted early during the virus spread.

“All countries are facing the same problem. You think you have it under control but it’s very hard to control,” he said.

“The more restrictions you have, the less the virus spreads; the more you release the restrictions, the more the virus spreads. It has to - people are going to work and so on, you expect they would be mingling and so you get the virus spreading. So it’s going to happen - we always knew that and we planned for it, it’s not something we didn’t know.

“The problem is that it’s not sustainable to maintain restrictions, where you close businesses. There has to be a point where you carry on and economy has to restart and so on.”

'People have gotten tired'

While many countries implemented lockdown regulations in a bid to flatten the curve, a Johannesburg-based expert warned that based on the amount of strain the lockdown has had on the public, people were bound to relax their caution and prioritise their livelihoods - and this could result in a quickening of the spread.

Valerie Keyser, head of HIV Advanced Clinical Care at Witkoppen Clinic in Fourways, Johannesburg, said pandemic had taken a toll on many people.

“We have patients who are keen and keeping up with the updates and they are maintaining it [their caution]. But a lot of people have gotten tired,” she said.

“I think people care more about something if it’s close to home. If you had an experience of someone close to you being positive, it changes everything. Our cases are going up. Soon most people will know someone who is positive.”

She said it was difficult for people to follow the regulations as they naturally craved - and had - freedom before the pandemic hit.

“If it affects one’s livelihood, people are bound to take the risk and go on with their lives.”

Keyser likened the attitude to the HIV/Aids health campaign, in that people started off cautious and adhering to protection methods, but eventually got tired.

While South Africa had invested many resources towards testing, with 1,353,176 tests done so far (of which 25,116 were in the past 24 hours), Abdool Karim said it had done enough, but no one could fully prepare for what’s to come.  

“No country will ever be prepared for the rapid way in which this virus grows. But I think we have prepared sufficiently, I think we have got to a point where quite a lot of work has been done. There will always be things that still need to be done, but I think we’ve made good progress.”

Abdool Karim said the country could in the coming months maintain the current 2% case fatality rate as the health system was not heavily compromised.

“Overall, South Africa has actually been in a pretty good position, compared to other countries with regards to the number of deaths - and that’s a reflection of the fact that we were able to flatten the curve and so our hospitals haven’t been dramatically overwhelmed with cases, including in the Western Cape.

“So we have been able to cope. Most of the patients have been recovering quite well. Our overall case fatality rate is about 2%, which is well in line with what we see in the rest of the world and much better off than countries like UK, Sweden and so on.”