Omicron drives record rate of Covid infection in South African province

Officials say variant’s R number is believed to be above 6, though most cases are mild

The pace of Covid infections in the South African province of Gauteng is outstripping anything seen in previous waves, and officials say Omicron is now the dominant variant.

Angelique Coetzee, the chair of the South African Medical Association, said Omicron's R number, measuring its ability to spread, is believed to be above 6. The R number for Delta, the dominant variant globally, is estimated to be above 5.

Speaking to the BBC’s PM programme, Ms Coetzee said: “We know currently that the virus is transmissible. According to the scientists the R value is 6.3, I think.”

The chief scientist at the World Health Organisation (WHO) urged people not to panic, saying it was impossible to predict whether Omicron would become the dominant variant worldwide.


Soumya Swaminathan said South Africa's experience showed that Omicron "was highly transmissible", but added: "How worried should we be? We need to be prepared and cautious, not panic, because we're in a different situation to a year ago.

“Delta accounts for 99 per cent of infections around the world. This variant would have to be more transmissible to outcompete and become dominant worldwide. It is possible, but it’s not possible to predict.”

Positivity rates

In Gauteng, a populous province that includes Johannesburg and is the centre of the outbreak, public health officials say case positivity rates have climbed from 2 per cent in mid-November to 24 per cent this week.

However, most of the cases seen in the province so far, including by Ms Coetzee, have been described as mild and are in younger patients, who make up a significantly greater proportion of the country’s unvaccinated.

Prof Bruce Mellado, who advises the provincial government, told the Daily Maverick that health officials had seen such a rapid increase in cases in Gauteng over the past few weeks that they had had to recalibrate their projection models. The increase was at a rate not seen before, he said, not even in the third wave, which Prof Mellado described as a "very serious situation".

Other officials in the province described a 20 per cent rise in the seven-day rolling average of daily Covid cases, and increasing hospital admissions, driven by Omicron.

First reported by South African scientists to the WHO on November 24th, Omicron has prompted some countries to shut their borders, reimpose travel restrictions and ramp up vaccination programmes.

Among the concerns is whether Omicron might be infecting infants with more severe disease than previous variants after a rise in admissions of under-fives to some hospitals.

At a news conference on Friday, Waasila Jassat, of the National Institute for Communicable Diseases, said: “We’ve seen quite a sharp increase [in hospitalisations] across all age groups, particularly in the under-fives. The incidence in those under-fives is now second highest, and second only to the incidence in those over 60.”

However, the number of infant cases remains relatively small, and it is unclear how many of those hospitalisations were due to Omicron.

Lower rate

Despite a rise in virus-related hospital admissions in South Africa, deaths appear to be increasing at a lower rate than during the country's third wave of Covid. This was underlined by a statement from the WHO on Friday, saying it had yet to see any reports of deaths related to Omicron.

Amid increasing evidence that current vaccines are likely to offer a high level of protection against serious disease from the variant, the chief executive of Germany’s BioNTech said it should be able to adapt its vaccine relatively quickly in response to Omicron.

Ugur Sahin told the Reuters Next conference on Friday that vaccines should continue to provide protection against severe disease despite mutations. "This variant might be able to infect vaccinated people. We anticipate that infected people who have been vaccinated will still be protected against severe disease," Sahin said.

He said mutations in the virus meant it was more likely that annual vaccinations would become the norm, as is the case with seasonal flu, and that new vaccines would be needed, although it was not yet clear when.

The WHO called on makers of Covid vaccines to gear up for the likelihood of needing to adjust their products to protect against Omicron. – Guardian