Where did Omicron Covid variant come from and where is it circulating?

on Dec2
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Doctor wearing PPE looks on before a house-to-house coronavirus testing drive 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’s 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 U.S. then became the 24th country to confirm its first case of omicron. It was detected in a fully vaccinated person in California, the Centers for Disease Control and Prevention confirmed on Wednesday.

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

The U.S., U.K. and EU, among others, responded to news of the variant last week by temporarily suspending flights from southern African countries, or introducing strict quarantines on anyone arriving from the region.

The move sparked anger in South Africa and has prompted criticism from the WHO, which said on Wednesday that such reactions could deter countries which sequence and report virus variants (like the U.K. and South Africa, where major Covid variants have been found) from being transparent in future.

Omicron circulating for a while?

The omicron variant, or B.1.1.529 as it’s formally known, was first reported to the WHO from South Africa on Nov. 24. The first known sample dated back to Nov. 9.

But there are now increasing signs that the variant was in circulation in other countries before South Africa’s health authorities alerted the world to its presence. There are a growing number of cases being discovered with no travel connection to the region, suggesting community transmission is taking place.

In Scotland in the U.K., for example, 9 cases have been detected that have been traced back to a “single private event” held on Nov. 20 and none of the individuals involved are believed to have any recent travel history to southern Africa.

Then, on Tuesday, the Netherlands said it had identified the omicron variant in two test samples taken in the country between Nov. 19 and 23 — before the variant was first reported by South Africa and travel bans came into place. It was initially believed that two flights that arrived in Amsterdam from South Africa last Sunday had brought the first cases of omicron to the country (there are now 14 confirmed cases in all).

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

Dr. Angelique Coetzee, chair of the South African Medical Association and the doctor who first raised the alarm over a possible variant, told the BBC Sunday that she did so after she started to see patients around Nov.18 presenting with “unusual symptoms” that differed slightly to those associated with the delta variant, the most virulent strain of the virus to date.

Meanwhile Botswana, one of the countries affected by Western travel bans in the wake of the variant, said last Friday that it first detected the variant on four foreign nationals who entered the country on a diplomatic mission on Nov. 7 (again, far earlier than it was reported by South Africa) as part of its regular Covid surveillance. It did not identify the foreign nationals’ home country.

Origin not in Africa?

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

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

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

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

“It’s only [with] the investigations that are being conducted that we’re going to know more about the origins of this virus,” he added.

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

“It seems that the majority of these countries that are [reporting omicron cases] now … are coming from abroad rather than here in Africa, so we don’t 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 likely been circulating for longer, and more widely, than initially thought.

“The origin of Omicron is still unknown, including the location where it first spread,” Moritz Kraemer, lead researcher on the Oxford Martin Programme on Pandemic Genomics at Oxford University, told CNBC Thursday.

“That in part is due to limited sequencing coverage and surveillance in some countries” he noted, adding that South Africa has a well established system of genomic surveillance.

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

Experts are widely expecting this variant to spread quickly given early indications from South Africa, where 74% of virus genomes sequenced in the last month belonged to the new variant.

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

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

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

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

While Danny Altmann, professor of immunology at Imperial College London, said he’d “certainly agree it’s a possibility” that the omicron variant was spreading earlier than November, and that there was no certainty it originate in South Africa.

“The point that it came to attention through rising cases and excellent sequencing around Gauteng [in South Africa] from the second week of November neither proves it arose near there or that this was the starting point.”

Correction: This story has been updated to reflect that the first U.S. case of the omicron variant was detected in California.

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