Severity of Omicron in SA is ‘being masked’ by 72% earlier infection rate

Leading scientists cautioned that the level of immunity against the coronavirus among SA’s population due to earlier infections may be masking the severity of illness caused by the Omicron variant.

Since the discovery of the variant in SA and Botswana was announced on November 25, hospitalisation rates in SA have risen, though at a much slower pace than in previous waves, even as cases are rising more rapidly.

The number of deaths has also been lower.

A recent seroprevalence survey in Gauteng, where the Omicron variant was first identified, showed 72% of the population had a previous Covid-19 infection, said Shabir Madhi, a vaccinologist at the University of the Witwatersrand. That compares with about 20% when the Beta variant emerged a year ago, said Madhi, who led trials of AstraZeneca Plc’s and Novavax Inc’s shots in SA.

“The evolution of the Omicron variant is coming at a very different stage of the pandemic,” Madhi said in an interview with the Global Health Crisis Co-ordination Centre.

“That is important to keep at the back of our minds when we see what is unfolding in SA and what we might see in other settings, which might have a very different epidemiology.”

Unnoticed infections

Official statistics don’t reflect the extent of the pandemic’s impact on SA, with just 3.2-million positive tests and about 90,000 deaths. Excess deaths, a measure of mortality compared with a historical average, show about 275,000 people may have died from the disease.

The disparity between official statistics and the likely extent of infections is more pronounced in SA, though not unique. The US Centers for Disease Control estimates that over the course of the pandemic until September, there were 146.6-million infections and 921,000 deaths as a result of Covid-19. Official statistics show more than 50-million infections and 799,000 deaths.

Madhi’s hypothesis is backed by other scientists. 

“You have large pockets of population immunity,” Tulio de Oliveira, who runs two gene-sequencing institutes in SA, said in an interview with CBS News on December 12.

“We’re going to have to tease apart if the mild cases are due to young people getting infected or if the previous population immunity from infection and vaccination are responsible for decreasing the number of hospitalised individuals.”

About 6,000 people are in hospitals in SA with Covid-19, about a third of the number at the peak of the second and third waves. Daily cases are now close to record levels.

“That could be due to the fact that immunity in the country is high either from natural immunity, from past infection or from vaccinations,” Barry Schoub, chairperson of the ministerial advisory council on vaccines, said in an interview with Sky News.

Of SA’s 60-million people, about 26% are fully vaccinated, compared to 70% in the UK.

While Omicron has, in early studies, shown it can evade antibodies produced by vaccinations or previous infections more easily than previous variants, Madhi said  immunity may stem from protection by T-Cells, which kill infected cells.

“In SA there is seemingly significant population protection against severe Covid-19 due to underpinning T-cell immunity, despite Omicron being antibody evasive,” he said. 

Beta variant

SA’s experience with Omicron may again raise the concept of herd immunity, whereby enough of the population has been vaccinated or had a previous infection to blunt the impact of waves of infection. However, the ability of the coronavirus to mutate and the different paths the pandemic has taken around the world may make that elusive.

“The data coming from SA are very encouraging,” said Sam Fazeli, senior pharmaceutical industry analyst for Bloomberg Intelligence.  

“Let’s not forget SA had a wave of infections with the Beta variant, which was not seen elsewhere. This may make a difference to the response to Omicron.”

More stories like this are available on bloomberg.com