The things we don’t know about the emergence of the omicron variant

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As flight KL592 was in the air between Johannesburg and Amsterdam on Friday, the rules of the pandemic changed. 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 travelers from southern Africa; suddenly, those onboard KL592 were persona non grata.

Dutch officials said 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. The Dutch weren’t the only ones to discover the variant in South Africa.

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.

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. 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. A coronavirus specimen taken by researchers in South Africa on Nov. 8 was found to have the variant according to the GISAID databank. The aggressive sequencing response of South Africa has resulted in scores more variant cases being found.

Countries have responded with praise for South African researchers, but also blanket travel restrictions on the nation and its neighbors. 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. This has been hard for many people to take.

“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 of the study were made public as soon as we knew 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. South Africa stands out from many other countries.

South Africa, the second largest economy in sub-Saharan Africa, is far ahead with nearly 25 percent of the population fully vaccinated. Pfizer, a drugmaker, also stated this week that Malawi, Mozambique and Namibia were among the countries banned from traveling by the United States. They requested for the delivery of vaccines to be held up due to difficulties with the uptake.

But as The Post’s Yasmeen Abutaleb and Lesley Wroughton wrote this week, the debate is more complex. In the queue for vaccines, low-income and middle-income countries like Africa continue to lag behind high-income wealthy nations. Experts believe that hesitancy is interconnected with supply problems. This could be due in part to delays in vaccines and the need to get them.

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. Later, officials admitted that it was an error and the samples had been taken in November. Only 2% of Nigerians are 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. Alpha was found in Britain while alpha was discovered in India. The fast-growing delta strain that has caused such severe damage in the past year is still unknown.

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. The countries returned to blanket travel bans despite the protests of African nations and the more severe warnings by the WHO. Many countries, including the United States have started to reconsider testing and quarantine at their borders. This is in accordance with WHO recommendations, but also creates disruption to travel and businesses.

Some countries are operating in the shadow of delta. U.K. 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 one of the first countries to ban southern Africa. Given the number of mutations which could affect immune response, political leaders will take a risk and overreact.

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. Given the many unknowns about micron, it is possible that prudence might be better than panic.

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