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

A doctor wearing PPE watches ahead of a door-to-door coronavirus testing campaign July 21, 2020 in Lima, Peru.

Raul Sifuentes | Getty Images News | Getty Images

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 a time.

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

The United States 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 are UK, France, Israel, Belgium, Netherlands, Germany, Italy, Sweden, Denmark, Australia, Canada, Hong Kong and a number of southern African countries.

The US, UK and EU, among others, responded to the variant’s announcement last week by temporarily suspending flights from southern African countries or introducing strict quarantines for any person coming from the region.

The move sparked anger in South Africa and drew criticism from the WHO, which said on Wednesday that such reactions could deter countries that are sequencing and reporting virus variants (such as the UK and South Africa, where major variants of Covid have been found) to be transparent. in the future.

Omicron has been around for a while?

The omicron variant, or B.1.1.529 as it is officially called, was first reported to the WHO in South Africa on November 24. The first known sample dated from November 9.

But there are now growing signs that the variant was in circulation in other countries before South African health authorities alerted the world to its presence. An increasing number of cases are being discovered unrelated to travel to the region, suggesting that community transmission is taking place.

In Scotland in the UK, for example, 9 cases have been detected which date back to a “one-off private event” held on November 20 and none of those involved appear to have a history of recent travel to southern Africa.

Then, on Tuesday, the Netherlands said it had identified the omicron variant in two test samples taken from the country between November 19 and 23 – before the variant was first reported by South Africa and that travel bans are not put in place. Two flights that arrived in Amsterdam from South Africa last Sunday were initially thought to have brought the first cases of omicron to the country (there are now 14 confirmed cases in total).

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

Dr Angelique Coetzee, president of the South African Medical Association and the first doctor to sound the alarm on a possible variant, told the BBC on Sunday that she had done so after she started seeing patients worms Nov. 18 showing “unusual symptoms” that differed slightly from those associated with the delta variant, the most virulent strain of the virus to date.

Meanwhile, Botswana, one of the countries hit by Western travel bans as a result of the variant, said last Friday it first detected the variant in four foreign nationals who entered the country. on a diplomatic mission on November 7 (again, long before it was reported by South Africa) as part of its regular Covid surveillance. He did not identify the country of origin of the foreign nationals.

Origin not in Africa?

At a press briefing organized by the WHO Africa office on Thursday, regional experts from the United Nations agency told CNBC that the origin of the omicron variant was unknown and they criticized the travel restrictive measures imposed on southern African countries.

“Our surveillance system in the world is not yet perfect,” Dr Abdou Salam Gueye, regional director of emergencies for the WHO Africa office, told CNBC on Thursday during a press briefing.

“When we detect a variant or a virus… we will usually detect it weeks after it begins to evolve. The only thing we’re sure of when a country detects a virus is that that country’s surveillance system is good. That’s what happened in southern Africa, so it discourages the travel ban even more because… it’s like a move against a good surveillance system. “

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

“It’s only [with] the investigations that are being carried out that we will find out more about the origins of this virus, “he added.

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

“It seems that the majority of those countries that are [reporting omicron cases] now … are coming from overseas rather than here in Africa so we don’t know where it started and we need some really good scientific evidence to further study the molecular evolution of the omicron variant. “

Experts based in Europe tend to agree that omicron has probably 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, principal investigator of the Oxford Martin Pandemic Genomics Program at the University of Oxford.

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

“Personally, I don’t think there has been a wide, undetected release for a very long time,” Kraemer said. However, he added that he expects the number of countries where omicron transmission is imported and local to be much more than reported.

Experts largely expect this variant to spread quickly given the first indications from South Africa, where 74% of the viral genomes sequenced last month belonged to the new variant.

Lawrence Young, professor of molecular oncology at the University of Warwick, told CNBC on Wednesday that “it is not surprising that omicron is circulating more widely and for longer than previously reported.”

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

Some epidemiologists have speculated that the omicron variant may have started to spread internationally around the end of October, a hypothesis endorsed by other experts interviewed by CNBC.

Paul Hunter, professor of medicine at the Norwich School of Medicine at the University of East Anglia, told CNBC on Wednesday that, given that the first known omicron sample was taken on November 9 in South Africa, ” it is clear that the infection must have circulated a little before that, unless the index case was the person to whom the variant progressed, but probably not much sooner. “

While Danny Altmann, professor of immunology at Imperial College London, said he would “certainly agree that it is possible” that the omicron variant has spread earlier than in November and that there was no certainty that it came from South Africa.

“The fact that it has gained attention thanks to the increase in cases and excellent sequencing around Gauteng [in South Africa] from the second week of November does not prove either that he was born near there or that it was the starting point. “

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

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