Where did the Omicron Covid variant come from and where does it circulate?

Doctor wearing PPE looks ahead to a house-to-house test drive with coronavirus on July 21, 2020 in Lima, Peru.

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LONDON – As more cases of the new omicron Covid variant emerge around the world, experts say it is likely that the variant, first identified in South Africa last week, had already been circulating for some time.

The World Health Organization said on Wednesday that at least 23 countries from five of the six WHO regions have now reported cases of omicron, “and we expect that number to grow.”

The United States then became the 24th country to confirm its first case of omicron. It was discovered in one fully vaccinated person in North Carolina, the Centers for Disease Control and Prevention confirmed Wednesday.

Other countries that have identified variant it United Kingdom, France, Israel, Belgium, Netherlands, Germany, Italy, Sweden, Denmark, Australia, Canada, Hong Kong and a number of countries in southern Africa.

Among others, the US, UK and EU responded to the news of the variant last week by temporarily suspending flights from South African countries or imposing strict quarantines for anyone arriving from the region.

The movement sparked outrage in South Africa and has given rise to criticism from the WHO, which on Wednesday said such reactions could deter countries sequencing and reporting virus variants (such as the UK and South Africa, where large Covid variants have been found) from being transparent in the future.

Omicron circulating for a while?

The Omicron variant, or B.1.1.529 as it is formally known, was first reported to the WHO from South Africa on 24 November. The first known sample dates back to November 9th.

But there is now growing evidence that the variant was in circulation in other countries before South Africa’s health authorities made the world aware of its presence. There are a growing number of cases being discovered without a travel connection to the region, suggesting that community transfer is taking place.

In Scotland, UK, for example, 9 cases have been discovered which have been traced back to a “single private event” held on 20 November and none of the people involved are believed to have any recent travel history to southern Africa .

So, on Tuesday, Holland said it had identified the omicron variant in two test samples taken in the country between 19 and 23 November – before the variant was first reported by South Africa and travel bans came into place. It was initially assumed that two flights arriving in Amsterdam from South Africa last Sunday had brought the first cases of omicron to the country (there are now 14 confirmed cases in total).

On Tuesday, Germany also reported an omicron case of a man in Liepzig who had not been abroad, nor had contact with anyone who had been.

Dr. Angelique Coetzee, president of the South African Medical Association and the doctor who first sounded the alarm over a possible variant, told the BBC on Sunday that she did so after she began seeing patients around November 18 with “unusual symptoms” that differed slightly from those associated with the delta variant, the most virulent virus strain to date.

Meanwhile, Botswana, one of the countries affected by Western travel bans in the wake of the variant, said last Friday that the variant was first discovered on four foreign nationals entering the country on a diplomatic mission on November 7 (again, much earlier than reported by South Africa) as part of its regular Covid monitoring. It did not identify the home country of the foreign nationals.

Origin not in Africa?

At a press briefing held by the WHO Africa Office on Thursday, UN agency regional experts told CNBC that the origin of the omicron variant was unknown and they criticized restrictive travel measures imposed on South African countries.

“Our global surveillance system is not perfect yet,” said Dr. Abdou Salam Gueye, regional emergency director of the WHO’s Africa office, told CNBC on Thursday during a press briefing.

“When we detect a variant or virus … usually we will detect it weeks after it started developing. The only thing we are sure of when a country detects a virus is that the country’s surveillance system is good. It is “what happened in southern Africa, so it discourages the travel ban even more because … it’s like a measure against a good surveillance system.”

He added that it was “not unexpected” that cases were now being discovered in Europe.

“It is only [with] the studies that are being conducted, we will know more about the origin of this virus, “he added.

His colleague, Dr. Nicksy Gumede-Moeletsi, a senior virologist at the WHO’s Africa office, told CNBC that the number of countries reporting the omicron variant increased daily.

“It seems that the majority of these countries are [reporting omicron cases] now … coming from abroad instead of here in Africa, so we do not know where it started, and we need very good scientific evidence to study the molecular evolution of the omicron variant further. “

Experts based in Europe tend to agree that omicron has probably been circulating for longer and more widely than first assumed.

“The origin of Omicron is still unknown, including the place where it first spread,” Moritz Kraemer, lead researcher on the Oxford Martin program on pandemic genomics at Oxford University, told CNBC on Thursday.

“This is due in part to limited sequencing coverage and monitoring in some countries,” he noted, adding that South Africa has a well-established system for genomic monitoring.

“I personally do not think there has been wide undiscovered circulation for a very long time,” Kraemer said. He added, however, that he expects the number of countries with imported and local transmission of omicron to be much larger than reported.

Experts largely expect that this variant will spread rapidly given early indications from South Africa, where 74% of the virus genomes sequenced in the last month belonged to the new variant.

Lawrence Young, a professor of molecular oncology at Warwick University, told CNBC on Wednesday that “it’s no surprise that omicron has been circulating wider and longer than previously reported.”

“Once a variant is identified, especially one that is likely to be more contagious, it will have spread far beyond the few original cases and countries. That is the nature of infectious diseases in a world where international travel is so common, ” he said.

Some epidemiologists have speculated that the omicron variant could have started spreading internationally around the end of October, a hypothesis that other experts have spoken to by CNBC.

Paul Hunter, a professor of medicine at the Norwich School of Medicine at the University of East Anglia, told CNBC on Wednesday that given the earliest known omicron sample was taken on November 9 in South Africa, “so clearly the infection must have circulated a little before that, unless the index case was the person where the variant evolved, but probably not much earlier. “

While Danny Altmann, professor of immunology at Imperial College London, said he “certainly agrees that it is a possibility” that the omicron variant spread earlier than November and that there was no certainty that it originates from South Africa.

“The point that it came to attention through increasing cases and excellent sequencing around Goateng [in South Africa] from the second week of November proves neither that it originated nearby nor that this was the starting point. “

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