Johnson & Johnson’s Covid vaccine was supposed to be one of Africa’s most important weapons against the coronavirus.

The New Jersey-based company agreed to sell enough of its inexpensive single-shot vaccine to eventually inoculate a third of the continent’s residents. And the vaccine would be produced in part by a South African manufacturer, raising hopes that those doses would quickly go to Africans.

That has not happened.

South Africa is still waiting to receive the overwhelming majority of the 31 million vaccine doses it ordered from Johnson & Johnson. It has administered only about two million Johnson & Johnson shots. That is a key reason that fewer than 7 percent of South Africans are fully vaccinated — and that the country was devastated by the Delta variant.

At the same time, Johnson & Johnson has been exporting millions of doses that were bottled and packaged in South Africa for distribution in Europe, according to executives at Johnson & Johnson and the South African manufacturer, Aspen Pharmacare, as well as South African government export records reviewed by The New York Times.

Glenda Gray, a South African scientist who helped lead Johnson & Johnson’s clinical trial there, said companies needed to prioritize sending doses to poorer countries that were involved in their production. “It’s like a country is making food for the world and sees its food being shipped off to high-resource settings while its citizens starve,” she said.

Many Western countries have kept domestically manufactured doses for themselves. That wasn’t possible in South Africa because of an unusual stipulation in the contract the government signed this year with Johnson & Johnson. The confidential contract, reviewed by The Times, required South Africa to waive its right to impose export restrictions on vaccine doses.

Popo Maja, a spokesman for the South African health ministry, said the government was not happy with the requirements in the contract but lacked the leverage to refuse them. “The government was not given any choice,” he said in a statement. “Sign contract or no vaccine.”

Johnson & Johnson had always planned for some vaccines produced by Aspen to leave Africa, but it has never disclosed how many doses it was actually exporting. The export records reviewed by The Times show that Johnson & Johnson shipped 32 million doses in recent months, although that does not capture the full number that have left South Africa.

Germany in April received shots produced by Aspen, a spokesman for Germany’s health ministry said. In June and July, Spain received more than 800,000 doses, according to the country’s health ministry.

Critics say the shortfall in South Africa partly reflects a power imbalance between a giant company and a desperate country.

“The disproportionate amount of power that Johnson & Johnson has exercised is really concerning,” said Fatima Hassan, a human rights lawyer in South Africa. “It is harming our efforts to get speedy supplies into the system.”

The picture is bleak across the continent. While several African countries received small initial shipments of Johnson & Johnson doses last week, they are a sliver of the 400 million doses that the African Union has ordered or has the option to order for its member countries. About 2 percent of Africans are fully vaccinated.

Johnson & Johnson’s chief scientific officer, Dr. Paul Stoffels, said the Aspen plant is part of a production network in which vaccines are routinely shipped between countries for manufacturing, quality inspection and delivery.

“We have done our best to prioritize South Africa as much as we can,” he said. He noted that Johnson & Johnson early this year provided about 500,000 doses to vaccinate South African health care workers. He said the Aspen plant would exclusively supply doses to African countries later this year.

Aspen is responsible for the final stage of vaccine production, a process known as “fill and finish.” The company receives mass quantities of the vaccine, bottles it into vials and then packages it for final inspections and delivery.

Some of Aspen’s doses were never used because of worries they might have been contaminated at the Baltimore plant that handled their first stage of production, according to Johnson & Johnson and Aspen executives. The problems at that plant, run by Emergent BioSolutions, wreaked havoc on Johnson & Johnson’s vaccine supplies, leading the company to fall behind on orders all over the world.

Stephen Saad, Aspen’s chief executive, blamed the lack of South African doses on the Emergent plant. He said Aspen could not control where its doses were sent, but “I would have liked to see it all go to Africa.”

Aspen is now finishing doses that were made at a plant in the Netherlands, with 40 percent of those doses going to Europe and the remaining 60 percent to Africa through the end of September. Previously, the plan was for only 10 percent to go to the continent, but the European Union agreed to change the distribution in light of South Africa’s crisis, said Daniel Ferrie, a spokesman for the European Commission.

South Africa’s vaccination campaign has accelerated in recent weeks, thanks largely to Pfizer doses ordered by the government and shots donated by the United States. But about four million of the country’s 60 million residents are fully vaccinated.

That left the population vulnerable when a third wave of cases crested over the country. At times in recent months, scores of Covid-19 patients at Helen Joseph Hospital in Johannesburg were waiting in the emergency department for a bed, and the hospital’s infrastructure struggled to sustain the huge volumes of oxygen being piped into patients’ lungs, said Dr. Jeremy Nel, an infectious-disease doctor there.

“The third wave, in terms of the amount of death we saw, was the most heartbreaking, because it was the most avoidable,” Dr. Nel said. “You see people by the dozens dying, all of whom are eligible for a vaccine and would’ve been among the first to get it.”

Critics say South Africa’s government shares blame for the low rate of vaccinations. Early on, the government relied on a United Nations-backed clearinghouse for vaccines that has fallen behind on deliveries. South Africa was slow to enter negotiations with manufacturers for its own doses. In January, a group of vaccine experts warned that the government’s “lack of foresight” could cause “the greatest man-made failure to protect the population since the AIDS pandemic.”

Johnson & Johnson’s deal with Aspen was announced in November. Aspen’s facility in Gqeberha, on South Africa’s southern coast, was the first site in Africa to produce Covid vaccines. (Other companies subsequently announced plans to produce vaccines on the continent.)

South African officials hailed Aspen’s involvement as indispensable.

Aspen “belongs to us as South Africans, and it is making lifesaving vaccines,” South Africa’s president, Cyril Ramaphosa, said during a visit to Aspen’s plant in March. He said he had pushed Johnson & Johnson to prioritize the doses made there for Africans.

“I want them now,” Mr. Ramaphosa added. “I’ve come to fetch our vaccines.”

The Johnson & Johnson vaccine became even more important in February when the results of a clinical trial suggested that the vaccine from AstraZeneca offered little protection from mild or moderate infections caused by the Beta variant that was circulating in South Africa.

Weeks later, Johnson & Johnson and the government signed a contract for 11 million doses. South Africa ordered another 20 million doses in April. That would be enough to vaccinate about half the country.

South Africa agreed to pay $10 per dose for the 11 million shots, according to the contract. That was the same price that the United States paid and slightly more than the $8.50 that the European Commission agreed to pay. The South African contract prohibited the government from banning exports of the vaccine, citing the need for doses to “move freely across national borders.”

Mr. Maja, the South African health ministry spokesman, said that absent that stipulation, the government might have stopped vaccine doses from leaving the country.

But the requirement put South Africa at a disadvantage compared with other places that were producing Covid vaccines.

The European Union introduced export controls this year to conserve scarce supplies. India halted exports produced by the Serum Institute, which was supposed to be a major vaccine supplier to poor countries. In the United States, officials said they didn’t ban exports, but they didn’t need to. The combination of the extensive vaccine production on American soil and the high prices the U.S. government was willing to pay meant that companies made the delivery of shots for Americans a priority.

Other benefits for Johnson & Johnson were embedded in the South African contract.

While such contracts typically protect companies from lawsuits brought by individuals, this one shielded Johnson & Johnson from suits by a wider range of parties, including the government. It also imposed an unusually high burden on potential litigants to show that any injuries caused by the vaccine were the direct result of company representatives engaging in deliberate misconduct or failing to follow manufacturing best practices.

“The upshot is that you have moved almost all of the risk of something being wrong with the vaccine to the government,” said Sam Halabi, a health law expert at Georgetown University who reviewed sections of the South African contract at the request of The Times.

Mr. Halabi said the contract’s terms appeared more favorable to the pharmaceutical company than other Covid vaccine contracts he had seen. South African officials have said Pfizer, too, sought aggressive legal protections.

The contract said Johnson & Johnson would aim to deliver 2.8 million doses to South Africa by the end of June, another 4.1 million doses by the end of September and another 4.1 million doses by the end of December. (The government expects the 20 million additional doses to be delivered by the end of this year, Mr. Maja said.)

The company has so far fallen far short of those goals. As of the end of June, South Africa had received only about 1.5 million of the doses from its order. The small number of doses that have been delivered to the African Union were on schedule.

The difficulties in procuring doses have revealed the limits of fill-and-finish sites, which leave countries dependent on vaccines from places like the European Union or the United States, said Dr. Salim Abdool Karim, who until March was co-chairman of South Africa’s ministerial advisory committee on Covid.

“Ultimately,” he said, “the solution to our problem has to be in making our own vaccines.”

Lynsey Chutel and Choe Sang-Hun contributed reporting.

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