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Data suggests Omicron variant ’mutated steadily, at a fairly leisurely pace’

File photo: The uncertain emergence of the virus represents a significant geopolitical problem, deepening the global division that has emerged during the pandemic. Picture: Ian Landsberg/African News Agency (ANA).

File photo: The uncertain emergence of the virus represents a significant geopolitical problem, deepening the global division that has emerged during the pandemic. Picture: Ian Landsberg/African News Agency (ANA).

Published Dec 2, 2021


By Adam Taylor

Washington - As flight KL592 was in the air between Johannesburg and Amsterdam on Friday, the rules of the pandemic changed.

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The spread of an alarming new Covid-19 variant soon to be named Omicron, first reported by South Africa, had prompted an abrupt reappraisal of the risks of international travel.

The Netherlands banned entry to travellers from southern Africa; suddenly, those onboard KL592 were persona non grata.

The Dutch government was following a familiar instinct, eventually taken by more than 30 nations. By shutting down travel from southern Africa, it hoped to keep this new variant out. But that was futile.

Not only did the chaotic, crammed scenes involving KL592 and another flight by Dutch airline KLM apparently become a Petri dish for spreading the variant - it later emerged that the virus was already in the Netherlands.

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Dutch officials said on Tuesday that they had reviewed genetic sequencing data and detected the variant in a sample collected on Nov. 19 and another on Nov. 23, several days before the now infamous flights took off. And the Dutch aren't alone in finding the variant was in their country before South Africa raised the alarm.

According to tracking data from GISAID Initiative, a global database of coronavirus genome, of the two dozen or so countries that have reported cases of omicron, more than half first found the variant in samples taken before South Africa alerted the World Health Organization (WHO) on Nov. 25.

The Centers for Disease Control and Prevention said on Wednesday that the first case of the new omicron variant on US soil has been identified in California in a traveller who returned from South Africa on Nov. 22.

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A comprehensive understanding of omicron's spread may be impossible - the United States is only sequencing and sharing around 3.6% of its coronavirus samples, according to analysis of GISAID data by The Washington Post, meaning that many samples are not studied closely for variants.

And many other nations lag even further behind.

The uncertain emergence of the virus represents a significant geopolitical problem, deepening the global division that has emerged during the pandemic.

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Omicron has heightened anger over how wealthy nations have hoarded vaccines at the expense of poorer ones, while countries in southern Africa have accused nations of "Afrophobia" and "racism" for imposing blanket travel bans.

Right now, the earliest known cases of omicron were found in South Africa. On Nov. 8, researchers in the country took a coronavirus sample that was subsequently found to contain the variant, according to the GISAID database. Scores more cases of the variant have been found there since, in part due to the nation's aggressive sequencing responses.

Countries have responded with praise for South African researchers, but also blanket travel restrictions on the nation and its neighbours. Some banned lists have included not only countries that have recorded cases of omicron, but also ones that have not, such as Zimbabwe and Namibia. It's been a bitter pill for many to swallow.

"I can sympathize with the knee-jerk reaction that if you hear there is something new and potentially nasty, you want to keep it out. The problem is that South Africa, at this stage, feels very much the victim of their own good deeds," Wolfgang Preiser, head of medical virology at Stellenbosch University in South Africa, told NPR on Wednesday.

"The results were publicized the moment we were sure about it. And this is actually enabling other countries to look out for it."

The idea of a "South African" variant has added fuel to a bitter debate about vaccine equality during the pandemic.

As a continent, Africa is lagging far behind in the global vaccination race, with just 7 percent of the continent fully vaccinated compared with 42 percent of the entire world. But South Africa is different than many of its neighbours.

South Africa, the second largest economy in sub-Saharan Africa, is far ahead with nearly 25 percent of the population fully vaccinated.

Drugmaker Pfizer also said this week that five of the eight countries included in a travel ban imposed by the United States - Malawi, Mozambique, Namibia, South Africa and Zimbabwe - had asked for deliveries of doses to be delayed due to problems with uptake.

But as The Washington Post's Yasmeen Abutaleb and Lesley Wroughton wrote this week, the debate is more complex. Low- and middle-income nations like those in Africa are persistently behind wealthy high-income nations in the line for doses. Problems with hesitancy are intertwined with supply issues, some experts argue, in part due to halts in vaccinations due to waits for doses.

Early cases have also been found in Botswana, where polls show high levels of acceptance of vaccination but less than 1 in 3 have been fully vaccinated.

Nigeria set off a flurry of interest on Wednesday after official data suggested that the country had found cases of omicron in October.

Officials later explained that this was a mistake and the samples were from late November. Less than 2% of Nigeria is fully vaccinated.

A hunt for the precise emergence of omicron may go nowhere. The origin of the original Covid-19 strain, first detected in Wuhan, China, remains a subject of fierce international disagreement.

Another variant, alpha, was initially detected in Britain, while the fast-spreading delta variant that caused so much damage earlier this year was first identified in India.

It isn't clear how long omicron was circulating below the radar, but as The Post's Joel Achenbach wrote this week, the data suggest that the virus "mutated steadily, at a fairly leisurely pace."

Scientists are as interested in the "how" the variant developed as the "where." Some researchers have theorized that it could even have evolved in an animal before being passed to humans.

If the variant was unexpected, the reflex reaction was not. Despite the complaints from African nations and more stern warnings from the WHO, countries reverted to blanket travel bans.

Many, including the United States, have begun to rethink testing and quarantine measures at their borders, which is more in line with WHO recommendations though also causes disruption to travel and business.

Some countries are operating in the shadow of delta. UK Prime Minister Boris Johnson was criticized this summer for keeping travel between Britain and India open as he courted Indian officials for a trade deal.

Britain was among the countries to swiftly impose a ban on southern Africa. Political leaders are willing to risk overreacting, given the alarming number of mutations that could impact immune responses.

But it is far from clear that the variant will be able to push out the dominant delta variant or what impact it would have. And given the number of things still not known about omicron, prudence may be a wiser strategy than panic.