Prof Salim Abdool Karim: SA was 'not caught with our pants down', while hospital numbers continue to show unvaccinated at higher risk

While experts are not seeing any “red flags” indicating that the Omicron variant of the coronavirus, identified by South African scientists last week, will cause more severe disease, hospital data from Gauteng is showing that the bulk of hospital admissions (87%) are unvaccinated people.

This was the message from a team of infectious disease specialists that briefed the public on Monday on the potential impact of the Omicron variant.

Professor Salim Abdool Karim, the director of the Centre for the Aids Programme of Research in South Africa, said if one looks at the global picture, the numbers are steadily rising across all continents.

Karim said while it looks like the Omicron variant will be more contagious there are “no red flags” yet to show that it will cause more severe disease. 

He said due to the excellent research by South African scientists, Omicron has been identified as a major driver behind the rapid increase in cases in Gauteng.

“We have been amazed at how fast the numbers are going up,” he said. “But we were not caught with our pants down. We expected and prepared for a fourth wave. [The scientists] gave us the best fighting chance by giving us information early. We didn’t know exactly when it would come and what it would look like,” he said.

Karim said that what scientists know about Omnicron is that it has some mutations that they have seen before and know well.

One set of mutations changed the way the diagnostic PCR test responds. Others indicate the variant is more contagious. There are also some mutations that have been associated with an increased ability to evade the body’s own immune response.

“We know that this variant has mutations similar to those with increased immune escape,” Karim said.

He said that for some of Omicron’s mutations scientists have information to work with but for others the implications are unclear.

Karim said they are not sure if current vaccines will protect against infection and mild disease with Omicron, as there is some evidence that it can “escape” from antibodies. 

This answer, Karim stated, will be known within two to four weeks.

“But based on what we know, we can expect that we can still see high effectiveness of vaccines to prevent severe disease and hospitalisation,” he added.

He said it was also very hard to escape T-cell immunity produced by vaccines.

“We understand that different vaccines may have different levels of protection against variants,” Karim continued.

He said vaccines across the board have continuously provided excellent protection (above 90%) against severe disease and hospitalisation. 

“The last thing we need is panic and over-reaction,” he stressed. “We have dealt with variants before. Closing the borders has almost no benefit. This variant has already been detected in 11 countries. 

He said it was likely that this variant will be more contagious and South Africa might soon top 10,000 new cases a day.

“Our biggest challenge will be to stop super-spreading events — particularly indoors,” he said, adding that to do this it might be necessary to restrict indoor gatherings to those who are vaccinated.

Dr Michelle Groome from the National Institute for Communicable Diseases (NICD) said the cases and the positivity rate (the percentage of positive tests) have been increasing rapidly in the past two weeks.

She said most of this has been driven by case increases in Gauteng, Limpopo, Mpumalanga and North West and in younger age groups.

But, she added, it has started to spread to older people.

Groome said Gauteng has gone from less than 100 new cases a day to over 1,500 new cases a day. The province accounts for 80% of new cases in South Africa. 

Dr Waasila Jassat from the NICD said they have seen a significant increase in cases of under 18 to 49-year-olds and they were also starting to see an increase in hospitalisations. An increase in admissions to hospitals, however, usually lags a week or two behind an increase in cases because of the nature of Covid-19.

She said at this stage there had been no increases in hospitalisations in provinces other than Gauteng nor has there been an increase in the death rate due to Covid-19 related complications.

She said Tshwane had the most significant increase in admissions with eight covid-related deaths, but they had no data on whether these deaths were caused by the Omicron variant.

Jassat said there had been a sharp increase in admissions in both public and private sector hospitals in the past two weeks and were increasing across all age groups even though the largest number of admissions always are older people.

“Admissions with severe disease are still quite low,” Jassat added.

She said the majority of patients admitted to hospitals are unvaccinated.

Jassat also said they are also not seeing any signals that can indicate whether Omicron will cause more severe disease at this stage.

Dr Unben Pillay, a general practitioner in private practice in Gauteng said they have been seeing a sharp increase in the number of Covid-19 cases. He said prior to 19 November, the cases seen by GPs were down to almost zero.

“The cases are very mild,” he said, adding that the most common symptoms are dry cough, fever, night sweats, body aches and general malaise.

“We haven’t seen a big increase in complications or hospital admissions but it is still early days,” he added.

The acting director-general for the national department of health, Dr Nicholas Crisp said the low incidence of severe disease might be due to the fact that more people have been vaccinated than in any of the previous three waves. He added that they are only seeing low numbers of vaccinated people being infected.

He said it was “purely academic” to discuss when Gauteng or South Africa will enter the fourth wave. 

“We will head into the fourth wave,” he added.

Groome added that for all practical purposes Gauteng has entered the fourth wave and the rest of the country’s provinces will follow.

Jassat said they were linking their systems to the PCR data, as these tests detect the Omicron variant specifically. 

“This way we will be able to compare and note outcome and severity of disease between variants,” she explained.

She said they expect the task team on vaccine mandates to come up with key recommendations. 

“When we get the working group to make recommendations... that is what we expect, you will need proof of vaccination to go to a certain environment,” he said.

Crisp said they were also expecting a plan on how to proceed with rolling out booster shots by the end of the week.

Minister of Health, Dr Joe Phaahla, said the identification of the new variant had created a very difficult situation for the department but it was in the public interest to announce their findings.

Phaahla said he was aware that it had caused a lot of anxiety and that subsequent travel bans for a number of countries had made “life more difficult”. 

“There is no need to panic,” Phaahla said. “We have been here before. It is not new territory. We have 20 months’ experience in handling Covid-19,” he added. 

“It is better to deal with an enemy you know than with an enemy you don’t know,” he said. 

He stated that scientists were still coming to grips with how infectious the new variant is and also what the risk to different age groups will be, as well as understanding the risk for reinfection and increased breakthrough infections and the protection that will be provided by vaccines. 

Phaahla reiterated the call made by President Cyril Ramaphosa on Sunday night for all South Africans to get vaccinated urgently. DM/MC