The first eight weeks after South Africa was hit by coronavirus infections were an absolute nightmare, Dr Kerrigan McCarthy from the National Institute of Communicable Diseases said during a webinar hosted by the University of Cape Town on Wednesday.

She said the case detection became hopelessly overwhelmed. “Our helpline received between 20,000 to 30,000 calls in each 24-hour period.”

Their initial data entry plans were under-resourced and experts were inundated, with each sector of society seeking clarity and guidance.

“One of the unfortunate honours for the Western Cape was that it was the first in many respects. It was the first to peak and also to provide field hospitals and experience a massive impact on clinical services,” she said, adding that the province was also the first to enter a period “post-Covid”.

McCarthy said while the first official case was confirmed on March 4 she believed that a number of asymptomatic people brought the virus in much earlier and it had remained undetected.

“It was inevitable that we would have missed the first few cases.”

She said they believed that in the early stages of the outbreak many cases were imported from Europe, the US, the Middle East and China but never identified.

“Lockdown definitely helped to stop the importation of cases.”

McCarthy said she was sent to assist with the outbreak in Eastern Cape on 19 March. “The province was relatively late to register a first case,” she said, adding that once the outbreak started it spread quickly.

“In the Eastern Cape, one of the challenges was the delayed readiness of quarantine and isolation facilities and problems with social distancing on grant payment day. Contact tracing was difficult and there were problems in the supply chain with personal protective equipment, causing tensions with labour unions.”

 She said with contact tracing taking up to 13 days, in some cases it was rendered meaningless.

Soon, she added, this became a national problem.

She said currently about 600 tests are conducted per 100,000 of the population, with lower rates in Limpopo, and a progressive decline in the public sector turnaround time.

“The national positivity rate has declined from 30% to 20%,” McCarthy said. The highest positivity rate is now in Free State with Western Cape having the lowest and Gauteng also registering a low rate. She said that their data shows that children under 18 were not affected extensively, with their incidence risk of Covid-19 being low.

“The models thankfully got it wrong,” McCarthy said. “If the models held true we would have had over a million cases by now. We have 600,000.”

She said the modelling consortium was considering the reasons for this, and that these could include a residual immunity to coronaviruses, and the impact of non-pharmaceutical measures like personal distancing, wearing masks and washing hands.

She said new models are looking at a possible second wave of infections in the country. There were various factors that could see a second outbreak of coronavirus infections, but there is a lot of uncertainty. However, countries where an early lockdown was implemented were less likely to face a second wave.

Hassan Mahomed, a public health specialist from Stellenbosch University, said the data shows that 80% of SA’s population remains susceptible to Covid-19. “That does put us at a risk of a second wave or further outbreaks.”

He added that it was of paramount importance that health services that were neglected during the outbreak be brought back on board as soon as possible. 

“Otherwise we will suffer a new crisis,” he said. “Given the weakness of our economy, we are facing further budget cuts. Prioritisation will be important. We need to think how best to do that.” 

McCarthy suggested that the country investigate adapting improved methods for contact tracing and engage with communities on how to make it more acceptable. 

“We also need to think of how we encourage isolation and quarantine.”

Professor Andrew Boulle, from UCT’s School of Public Health, said that in the Western Cape the positivity rate had dropped to 10%. 

“To put this in perspective, we are seeing 2,000 to 3,000 positive cases a week. There was a time when this was the number of new cases we had in a single day.”

He said a smaller but definite decline is also being observed in the number of infections among health workers.

“There is a consistent picture of a gradual decline,” he said, adding that similar patterns are being seen in the number of deaths and the use of bulk oxygen.

Mary-Ann Davies, from the University of Cape Town’s School of Public Health and Family Medicine, warned that SA was not “out of the woods yet”.

She said that South Africa needed a surveillance strategy that will pick up the start of a second wave of infections very quickly. This strategy will include testing patients seeking routine healthcare, like pregnant women, and people living with HIV who attend clinics for viral load testing.

“It will give us a sense of where we are,” she said.

She added that they will propose that wastewater testing be included in the surveillance strategy. 

“[This is]an exciting and novel way of tracking an outbreak,” Davies said, explaining that it will help to identify areas with active viral infections. 

She stressed that the most important part of responding to a possible second outbreak would be to put new cases in isolation and track those cases properly. It would, she said, be beneficial to expand the criteria for testing to include asymptomatic people in certain high-risk settings. MC