No, the WHO did not say the omicron variant originated in South Africa — it said South Africa reported it first

Over the Thanksgiving holiday weekend, the World Health Organization (WHO) announced a new, highly-mutated COVID-19 variant of concern, dubbed omicron. It announced that the new variant was first reported to the WHO by South Africa.

Many countries around the world, including the United States, responded by restricting travel to and from South Africa and other countries in southern Africa. 

Meanwhile, people have gone to Google to search for “South Africa variant” to find information on omicron. The South African government, its neighbors and some social media users have pushed back against claims that the variant originated in South Africa and the emerging label “South Africa variant.”

THE QUESTION

Did the World Health Organization say the omicron variant originated in South Africa?

THE SOURCES

• World Health Organization (WHO)
• Government of Botswana
• South Africa President Cyril Ramaphosa
• South Africa’s Department of Health
• European Centre for Disease Prevention and Control (ECDC) and health agencies in individual countries

THE ANSWER

No, South Africa was just the first country to report the new variant to the World Health Organization. That doesn’t mean the variant necessarily originated there.

WHAT WE FOUND

The WHO said the SARS-CoV-2 variant it named omicron was first reported to it by South Africa on Nov. 24. The first confirmed infection, however, was identified a couple of weeks prior in Botswana.

On Nov. 26, Botswana’s government explained in a statement that the new variant “was detected on four foreign nationals who had entered Botswana on the 7th November 2021, on a diplomatic mission. The quartet tested positive for COVID-19 on the 11th November 2021 as they were preparing to return.”

South Africa’s Department of Health supports this, stating the earliest sample was detected on Nov. 11 in Botswana.

“Such detection should not be confused with Botswana being the country of origin of the strain,” Dr. Edwin Dikoloti, Botswana’s health minister, said in a press conference. Officials from Botswana have not made public the country of origin of these diplomats, and contacts of the diplomats identified in Botswana so far have tested negative for COVID-19 and show no symptoms of the disease.

In a statement criticizing travel restrictions to and from South Africa and vaccine inequities, South Africa President Cyril Ramaphosa confirmed the first omicron infection in South Africa was identified soon after the first infections in Botswana. He said the emergence of the variant coincided with a rise in cases in South Africa, where about 35% of adults are fully vaccinated.

The governments of South Africa and Botswana have pushed back against border closures in response to the variant’s discovery, pointing out the WHO advises against such measures and the variant has already been identified in other regions of the globe.

As of Nov. 29, the European Centre for Disease Prevention and Control (ECDC) and the UK’s health department have confirmed infections of the omicron variant in nine European countries. Outside of Europe, cases have been confirmed in Canada, China and Israel. Some of the cases have been directly linked to travel to southern Africa, others have been linked to travel from elsewhere and a few of Israel’s suspected cases are not linked to travel at all.

The delay between omicron’s first confirmed infection and the date it was first reported has to do with the process of sequencing the virus’s genome and identifying its mutations. Now that scientists from South Africa have shared the variant’s genome with global health officials, other countries are able to identify the virus with tests and in past samples of the virus. The WHO is recommending countries investigate these past samples to find out where omicron may already be present in the community. Since then, the Netherlands announced it has discovered two samples of omicron from before South Africa reported it to the WHO with the oldest sample being from Nov. 19.

It’s likely more cases from early November will be identified as the omicron variant through these processes. As of Dec. 1, 2021, WHO Director-General Tedros Adhanom said 23 countries from five of six WHO regions have now reported cases of Omicron, and he expects that number to grow.

The exact origins of the variant are still unknown.

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