The identification of a new, highly-mutated variant of the coronavirus virus in southern Africa this week highlights the risk to global public health posed by large, unvaccinated populations in the developing world, where countries have struggled to get immunizations and the virus is spreading and evolving.

Overall, just 7% of people in Africa are fully vaccinated, compared with 42% of the global population, according to Our World In Data, a project based at Oxford University. In Europe and the U.S., vaccination levels are...

The identification of a new, highly-mutated variant of the coronavirus virus in southern Africa this week highlights the risk to global public health posed by large, unvaccinated populations in the developing world, where countries have struggled to get immunizations and the virus is spreading and evolving.

Overall, just 7% of people in Africa are fully vaccinated, compared with 42% of the global population, according to Our World In Data, a project based at Oxford University. In Europe and the U.S., vaccination levels are 67% and 58%.

That disparity, public-health officials say, helped open the door to the rise of this latest variant, which has more than 50 mutations—including 30 on the virus’s spike, a main target for vaccines—from the one that emerged in Wuhan, China, two years ago.

World Health Organization scientists on Friday declared the new strain, which they named Omicron, a “variant of concern” and said evidence suggests that it is more contagious and that it is able to infect people who have already had Covid-19 or been vaccinated.

The variant that is currently dominant world-wide, Delta, was first identified in India and sparked a surge that reached 400,000 cases a day there last spring, when vaccinations remained at low levels.

About a third of India’s population has now been fully vaccinated, yet vast areas of the developing world remain even further behind. Africa’s most populous country, Nigeria, has fully vaccinated just 1.7% of its 206 million people. Africa’s second-most populous country, Ethiopia, currently in the grips of a civil war, has covered just 1.2%.

Export bans imposed in India slowed the distribution of vaccines to developing nations; vials of a version of the AstraZeneca vaccine in Pune, India.

Photo: /Associated Press

Some public-health officials say they are worried the world risks being pulled into a dangerous cycle in which worrying new variants emerge in unvaccinated populations, prompting more highly-vaccinated countries to order up booster shots, making it more difficult to get doses to the developing world.

“We’re looking into a situation where high-income countries will keep getting regular boosters, while people in low-income countries haven’t even had their first dose,” said Alexandra Phelan, an adjunct professor of global and public-health law and ethics at Georgetown University.

To help close the gap, the Biden administration in May said it would support temporarily suspending patents and other intellectual property behind the vaccines. The idea was to let developing countries produce their own shots, for their own people.

Proponents of that, including South Africa and India, have been unable to reach agreement with opponents, including the EU, which says lifting patent protections would discourage investment in pharmaceutical research while not doing much to ease the pandemic.

Children between the age of 5 and 11 are now eligible for vaccines in Austria; a child receiving a shot in Vienna in November.

Photo: Georges Schneider/Zuma Press

In a statement Friday, President Biden called on countries to waive intellectual property protections for vaccines. “This news today reiterates the importance of moving on this quickly,” he said.

The new variant has already spread to several other southern Africa countries, as well as Europe and China, scrambling international air travel and pushing governments to reconsider lockdown measures they badly wanted to avoid.

Stocks, oil prices and government-bond yields all slumped on Friday as companies braced for the grim likelihood that pandemic disruptions will continue into 2022.

It isn’t clear where the new variant originated. South Africa has developed a thorough surveillance system, genetically sequencing coronavirus samples, to observe how the pathogen is changing, meaning that it may be the country that simply found the variant, not the place it emerged.

Africa’s most populous country, Nigeria, has fully vaccinated just 1.7% of its 206 million people; a man receiving a Moderna shot in Lagos in August.

Photo: Sunday Alamba/Associated Press

Africa isn’t alone in having big chunks of the population unvaccinated, either. South Africa, having covered 24% of its residents, will likely soon surpass Bulgaria, the least vaccinated EU country, which has ample supply thanks to Europe’s multibillion-dollar vaccine bulk purchases, but which has yet to persuade more than 25% of its population to get a shot.

What is clear, public-health experts say, is how much the pandemic recovery and the global economy, even in wealthy states, depends on increasing both supply and demand in poorer parts of the world where most people still aren’t being vaccinated.

For most of this year, Africa sat on the sidelines of the massive international vaccine rollout. Covax, the WHO-backed campaign to get doses to low-income countries, has managed to ship just 544 million doses, about a third of what it had planned to have sent by now.

Exports bans, manufacturing snafus, and the sweep of the more transmissible coronavirus variant Delta through India, the world’s largest vaccine maker, delayed it. Those obstacles are finally, tentatively lifting and Covax expects to have at least 400 million doses coming through the pipeline next month.

Manufacturers around the world are on track to produce a total of 12 billion doses by the end of the year, according to the International Federation of Pharmaceutical Manufacturers and Associations, an industry lobby. That is more than the 11 billion doses that the WHO says are needed to provide two doses to 70% of the human population.

After scientists identified a new variant of the virus causing Covid-19, countries restricted travel to and from southern Africa. WSJ’s Anna Hirtenstein explains that investors have turned to bonds and gold as they prepare for more potential disruption. Photo: Sumaya Hisham/Reuters The Wall Street Journal Interactive Edition

Still, huge orders from that supply are going to wealthy countries where they risk sitting on shelves. Poorer countries have less clarity on when their doses are scheduled to arrive.

As supply increases, authorities are finding new challenges, among them, demand. People in areas with low case loads—or a lack of confirmed Covid-19 infections because of spotty testing and hospital care—have been less pressed to get the shot.

Africa’s younger population has had far fewer confirmed Covid-19 deaths than the more elderly nations of Europe and the Americas, although official statistics likely vastly undercount the true toll. Public-health officials have spent decades struggling against vaccine hesitancy in deeply conservative areas like northern Nigeria, where a largely Muslim population is often broadly skeptical of the intentions of Western nongovernmental organizations.

“A lot of vaccines are coming in now and the uptake is challenging,” John Nkengasong, Cameroonian virologist and director of the Africa Centers for Disease Control and Prevention, told reporters yesterday.

Governments haven’t found the funds for public-awareness campaigns, and after a year of waiting for vaccines, big shipments have arrived at short notice, with little time to set up vaccination sites. Keeping doses suitably refrigerated has been a headache for countries where the electricity comes and goes.

Some African countries have asked Covax to delay their late-2021 shipments of vaccine into next year, so they can have time to set up the costly infrastructure to deploy them.

“The Covid-19 vaccine stands among humanity’s extraordinary scientific feats,” said Matshidiso Moeti, the WHO’s regional director for Africa. “In Africa, we’re gradually overcoming supply constraints.”

—Gabriele Steinhauser contributed to this article.

Write to Drew Hinshaw at drew.hinshaw@wsj.com