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Omicron Variant Drives Rise in Covid-19 Hospitalizations in South Africa Hot Spot


South Africa has the largest known Omicron-linked outbreak. On Monday, the main airport in Johannesburg was nearly empty.


Jerome Delay/Associated Press

JOHANNESBURG—The emergence of the Omicron variant of the coronavirus in South Africa has driven a sharp increase in Covid-19 hospitalizations in the country’s hot-spot province over the past two weeks, although fewer patients are being treated for severe disease than in previous surges, the country’s National Institute for Communicable Diseases said.

There has also been an unusually high number of hospitalizations of children under 2 years old around the capital, Pretoria, where cases started rising first, although some of these may be precautionary, the institute said.

Overall, the proportion of people diagnosed with Covid-19 who have been admitted to the hospital over the past two weeks is in line with other waves of infection in South Africa, which were driven by other variants, said Waasila Jassat, a public-health specialist at the NICD.

The data gives a first insight into what Omicron, which the World Health Organization declared a “variant of concern” last week, does to the human body and how that may differ from Covid-19 caused by other strains. But doctors and other experts cautioned that the overall number of patients so far remains too small—and their infections too recent—to draw firm conclusions on whether Omicron leads to milder or severe cases of Covid-19 than other variants.

Scientists and vaccine makers are investigating Omicron, a Covid-19 variant with around 50 mutations, which has been detected in many countries after spreading in southern Africa. Here’s what we know as the U.S. and others implement travel restrictions. Photo: Fazry Ismail/EPA-EFE/Shutterstock

South Africa is at the center of the race to understand the properties of the variant and whether it is more harmful than other versions of the coronavirus because some of the earliest cases were detected there just over two weeks ago, and it is the country with the largest known Omicron-linked outbreak. That means that the first hospitalizations resulting from the variant are likely to have happened only recently, given severe illness from Covid-19 takes up to two weeks from catching the virus to develop, and deaths lag even further behind.

As more countries world-wide found the variant, new information began to trickle in. In Israel, four people confirmed with the Omicron variant had been vaccinated three times. In the U.K., six Omicron cases were identified in Scotland, some who hadn’t traveled, indicating the variant had spread within the community.

Israel’s first case, identified on Friday, was a woman who had recently traveled to Malawi. Israel’s second case, identified Sunday, had traveled in South Africa. Two more were confirmed on Monday: a doctor who returned from a conference in England and another doctor who came into contact with him at the Tel Hashomer Hospital in central Israel. All currently have mild symptoms, according to statements from health officials and a spokesperson for the Tel Hashomer Hospital.

Israeli authorities are backtesting polymerase-chain-reaction tests carried out over the past few weeks, and are increasing genetic surveillance of current tests, purchasing 10 million PCR kits adapted specifically for the new variant. They are also expanding a program monitoring sewage for traces of the variant.

Health officials say they still don’t have enough local data to say anything meaningful. Their overall assessment, gleaned from the gathered data and their discussions with peers across the globe, including from South Africa, is that the variant is indeed more transmissible than previous variants.

In the U.K., where 11 confirmed Omicron cases—one of which had left the country—have been identified, the U.K. Health Security Agency is running full genomic sequencing on anyone who tests positive for the virus and lives in an area with a confirmed case. It is also sequencing anyone who recently returned from southern Africa and tested positive for the virus.

In South Africa, the average number of people admitted to the hospital with Covid-19 in Gauteng province—home to both Pretoria and the economic capital, Johannesburg—jumped to 49 daily during the two weeks ended Nov. 27, according to the NICD data. In the previous two weeks, the average daily number of Covid-19 admissions was 18. The number of daily deaths hasn’t changed, the data showed.

The first known South African cases of Omicron were detected on Nov. 11, a time when Covid-19 infections across the country were at their lowest level since the start of the pandemic. Since then, the daily number of recorded cases nationwide has risen sharply, from around 300 a day to 3,220 on Sunday.

Only a very small number of the current Covid-19 cases in South Africa have been confirmed as Omicron through genomic sequencing, the only surefire way to determine what variant caused an infection. But Omicron shows up differently from other variants in one of the widely used polymerase-chain-reaction, or PCR, tests, making it easier to track. Based on this method, South African experts say most recent cases in Gauteng appear to be caused by Omicron.

In the Netherlands, Red Cross vans transported travelers from South Africa who tested positive for Covid-19 to a hotel for quarantine.


Hollandse-Hoogte/Zuma Press

In a document setting out what actions governments should take against Omicron, the WHO warned on Monday that the variant had a high potential to spread further globally and could drive fresh surges of Covid-19 infections. The agency said it based this assessment on Omicron’s more than 50 mutations, some of which it said may give it the potential to escape immune responses triggered by vaccination and previous infection or be more contagious.

The agency advised governments to step up sequencing of virus genomes to track Omicron in their countries and rely on the markers in some commonly used Covid-19 tests that can flag the variant in a test sample. Countries should also get as many people as possible vaccinated, require social-distancing measures, such as indoor mask wearing, and prepare their health systems for a potential increase in infections, the WHO said.

The outbreak centered in Gauteng appears to have started among people of college age around Pretoria, a factor that further distorts early conclusions about the kind of disease Omicron causes. Young people are generally much less likely to fall seriously ill with Covid-19 than older people.

In South Africa, like in many other countries, young people are also much less likely to be vaccinated against Covid-19 than older age groups. On average, just over 24% of South Africa’s 60 million people are fully vaccinated.

People queue to be tested for Covid-19 in Johannesburg.


Jerome Delay/Associated Press

Dr. Jassat said around a fourth of patients admitted with Covid-19 in Gauteng were vaccinated.

Zooming into hospital admissions around the city of Pretoria provides some further insight, although it also means that the overall case load that can provide information becomes even smaller.

One thing that stood out to the specialists examining the data was the unusually high number of very young children who have been admitted to the hospital. Children generally only experience mild Covid-19, although the virus can be dangerous for very young babies.

The number of hospital admissions around Pretoria was highest for infants and children under 2, said Dr. Jassat. She added, however, that some of these children may have been admitted as a precaution. “We’re not sure if it’s related to the variant circulating,” she said.

No Covid-19 vaccines have been approved for children under 5. In South Africa, only people over 12 are currently eligible for vaccination. The country hasn’t started rolling out booster shots beyond healthcare workers who received one dose of the

Johnson & Johnson


“Vaccination of the adults around the children will likely protect the children as well,” said Dr. Jassat.

Unben Pillay, a doctor who runs a private practice in Gauteng who spoke at the same news conference as Dr. Jassat, said patients at his practice showed similar symptoms to those in previous waves. Those symptoms are mostly flulike, including fever and dry cough, said Dr. Pillay.

“We’ve started seeing an increase in cases over the past week,” he said.

Dr. Pillay said vaccinated patients he has treated over the past week generally showed milder symptoms and could be managed at home.

Write to Gabriele Steinhauser at

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Appeared in the November 30, 2021, print edition as ‘Omicron Sickens More in South Africa.’

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