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 Statespaid 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.”

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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Somalia Moves to Defuse Tensions Both at Home and Abroad

NAIROBI, Kenya — Days after Somalia’s president relented on plans to extend his term in office following street battles and international condemnation, his government announced Thursday that it would restore diplomatic relations with Kenya, ending a monthslong standoff that had injected an additional note of instability into an already-volatile region.

The Somali deputy minister of information said that Qatar had played a role in mediating between the two nations, and that the two sides would hold further talks in the near future on issues including trade and the movement of people.

The announcement, six months after Mogadishu severed relations with Nairobi, accusing it of “blatant interference” in its internal political affairs, came just days after tensions also ratcheted down on the domestic front.

On Saturday, President Mohamed Abdullahi Mohamed, facing huge domestic and international pressure, as well as infighting among rival security forces in the streets of the capital, backed down on a bid to extend his term and called for the resumption of election planning.

a statement, “The two governments agree to keep friendly relations between the two countries on the basis of principles of mutual respect for sovereignty and territorial integrity, noninterference in each other’s internal affairs, equality, cooperation and peaceful coexistence.”

Kenya’s government said Thursday that it welcomed efforts to normalize relations between the two countries.

The severance of diplomatic relations in December was provoked by a number of tensions, some new and some longstanding.

Most recently, in December, Kenya hosted the president of Somaliland, a breakaway region in the northwest that has yet to gain international recognition. Mogadishu also accused Nairobi of interfering in the electoral process in Jubaland, a region in southern Somalia where Kenyan troops are stationed as part of the African Union peacekeeping mission.

For years, the two countries have also tussled over a sizable area in the Indian Ocean, leading to a high-profile court case at the International Court of Justice that Kenya has boycotted.

a onetime state official in Buffalo, N.Y., who returned to his homeland and began stoking nationalist passions, was accused of trying to hold onto power at whatever cost.

extended his term in office by two years — a move his opponents said he had orchestrated. That set off fierce fighting in the streets of Mogadishu that displaced between 60,000 and 100,000 people, according to the United Nations.

But last Saturday, Mr. Mohamed relented, asking the country’s prime minister to lead preparations for an election as lawmakers nullified his term extension.

On Tuesday, Mr. Mohamed spoke with the leader of Qatar, whose government he has depended on for financial and logistical backing. He also met with Mutlaq bin Majed al-Qahtani, Qatar’s special envoy for counterterrorism and mediation of conflict resolution. Mr. al-Qahtani, who spent three days in the country, also met with other major political leaders.

met with President Uhuru Kenyatta on Thursday, said it was “not in the interest of Somalia and Kenya to have a less stable region.”

“We hope this step will bring prosperity to the two neighboring countries, their people, and the region,” he said.

Declan Walsh contributed reporting.

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Africa’s Vaccine Drive Is Threatened by India’s Supply Halt

NAIROBI, Kenya — The rapidly escalating coronavirus crisis in India is not only forcing hospitals to ration oxygen and sending families scrambling to find open beds for infected loved ones. It is also wreaking havoc on the global vaccination effort.

Nowhere is that more evident than in Africa.

Most nations were relying on vaccines produced by the Serum Institute factory in India. But the Indian government’s decision to restrict exports of doses as it deals with its own outbreak means that Africa’s already slow vaccination campaign could soon come to a near standstill.

Before India suspended exports, more than 70 nations received vaccines it manufactured, totaling more than 60 million doses. Many went to low- and middle-income countries through the Covax program, the global initiative aimed at ensuring equitable access to vaccines.

So far, Covax has delivered 43.4 million doses to 119 countries, but this represents only about 2 percent of the two billion doses it hopes to deliver this year, according to Andrea Taylor, an assistant director at the Duke Global Health Innovation Center.

according to the Africa Centers for Disease Control and Prevention.

Just six million doses have been administered in all of sub-Saharan Africa — fewer than in many individual U.S. states. The prospect of reduced supplies further complicates what was, for many African nations, an already daunting logistical challenge.

Many African governments prioritized administering first doses to more of their populations in the expectation that more doses would soon arrive. Now they are struggling with what to do if there are not enough vaccine supplies to give the full two-dose regimen that offers maximum prevention.

Countries like Rwanda and Ghana, which were among the first to receive doses from Covax, are about to exhaust their initial supplies. In Botswana, inoculations were temporarily halted in some areas this month after the allotted doses were finished. And Kenya, which has almost run out of its initial one million doses, said this week that it would seek to acquire Johnson & Johnson and Pfizer vaccines to continue its inoculation campaign. On Saturday, because of the delays, the country lengthened the timing between the administration of the first and second dose to 12 weeks from eight.

have run through more than two-thirds of their supplies, said Dr. Matshidiso Moeti, the World Health Organization’s regional director for Africa.

The African Union’s vaccination task force has secured funding to purchase up to 400 million Johnson & Johnson vaccines for member states — but those doses won’t start arriving until fall.

“More than one billion Africans remain on the margins of this historic march to end this pandemic,” Dr. Moeti said.

A spokesman for Gavi, which helps lead the Covax program, said in an email that it was in close contact with the Indian government about restarting vaccine shipments, but that “in terms of timing of next deliveries, we’re not able to confirm at this stage.”

Even as the United States sits on tens of millions of doses of the AstraZeneca vaccine — the most affordable vaccine in widespread use — African nations are turning to Russia and China for doses made in those countries, despite concerns about lack of clinical data on their efficacy and safety.

Amid the delays, some African countries are facing new and possibly deadlier waves of the pandemic. The Africa Centers for Disease Control and Prevention reported 2,155 deaths from the virus in the past week, up from 1,866 the week before.

In Nairobi, the capital of Kenya and home to one of the continent’s better health care systems, officials have warned of a scarcity of intensive-care beds and oxygen supplies. Last month, the Kenyan government ordered a new lockdown that has prompted anger over the restrictions’ economic impact.

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J. & J. to Resume E.U. Vaccine Rollout, With Warning of Rare Side Effect

BRUSSELS — Johnson & Johnson said Tuesday that it would resume the rollout of its coronavirus vaccine in Europe after the European Union’s drug regulator said that a warning should be added to the product indicating a possible link to rare blood clots, but that the shot’s benefits outweigh the risks.

The company decided to delay distribution in the bloc’s 27 member states last week, after regulators in the United States suspended use of the vaccine there amid concerns about the potential side effect.

The E.U. drug regulator’s endorsement — even with the caveat — not only clears a path for Johnson & Johnson in Europe, but could presage how the United States will handle the vaccine in the days to come.

On Friday, an advisory panel to the Centers for Disease Control and Prevention is to meet for a second to time to decide whether to recommend lifting a “pause” put on the vaccine’s use in the United States, perhaps with a similar warning.

had the Johnson & Johnson vaccine.

But some health experts worry that the headline-grabbing pause, which began over a week ago, might discourage some people from getting vaccinated, even though the risks from Covid-19 are far greater than the risk from a clot.

“You’ve put a scarlet letter on the Johnson & Johnson vaccine,” said Dr. Paul A. Offit, a vaccine expert at Children’s Hospital of Philadelphia.

After clotting concerns associated with another vaccine, produced by AstraZeneca, were reported in Europe, Dr. Offit noted, some grew leery of it, overestimating the threat. For the Johnson & Johnson vaccine, the clot risk has been put at an estimated one in a million.

“If you take a theoretical million people who are infected with Covid, five thousand will die,” Dr. Offit said. “Therefore, the benefits of this vaccine clearly outweigh its risks.”

a statement, the agency stressed the importance of treating the potential side effect and issued guidelines to health care professionals on the lookout for the rare clotting disorder. It listed symptoms to be vigilant for, including shortness of breath, chest pain, leg swelling, persistent abdominal pain, severe and persistent headaches or blurred vision, and tiny blood spots under the skin.

The temporary suspension of the Johnson & Johnson rollout in the European Union had added to the bloc’s vaccine rollout woes, but it was not as big a blow as the AstraZeneca issues have been.

Vaccination efforts have fallen behind in Europe partly because AstraZeneca, a British-Swedish pharmaceutical company that is a major component of the region’s inoculation efforts, was unable to deliver the number of doses expected in the first quarter of the year. Then its vaccine was suspended over the blood-clotting concerns.

Even though the authorities eventually declared that the benefits of the AstraZeneca vaccine outweighed risks, and advised E.U. members to use it, the damage had been done.

Pfizer-BioNTech vaccine, and was negotiating a new deal for future booster shots with the company for 2022 and 2023.

But while the impact for Europe may be cushioned, it could be a different story elsewhere. The Johnson & Johnson vaccine has been an important component of vaccination plans for countries around the world.

While it has not yet been rolled out at anything near the scale of AstraZeneca’s, some regions have pivoted to the shot amid AstraZeneca shortages. The African Union recently acquired 400 million doses.

The pause on Johnson & Johnson vaccinations in the United States, along with new restrictions on the use of AstraZeneca’s shot in Europe, rattled vaccination campaigns around the world relying on those vaccines. South Africa followed the United States in pausing Johnson & Johnson shots, though its health regulator in recent days recommended resuming its use.

U.S. health officials called for a pause in the vaccine’s use on April 13. Johnson & Johnson suspended its E.U. rollout immediately afterward, just as the first shipments of the shot were arriving in the region.

U.S. regulators and scientists are still studying the original reports of the clotting disorder and sifting through any new safety reports of possible cases of the clotting disorder. That effort has so far turned up little.

Dr. Rochelle P. Walensky, the C.D.C. director, said on Monday that health officials were investigating “a handful” of new, unconfirmed reports that emerged after the pause was recommended, to determine whether they might be cases of the rare blood clotting disorder.

“Right now, we are encouraged that it hasn’t been an overwhelming number of cases, but we are looking and seeing what has come in,” she said at a White House news conference.

Carl Zimmer contributed reporting from New Haven; Noah Weiland and Sharon LaFraniere from Washington; and Benjamin Mueller from London.

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Vaccine Hesitancy Leaves Doses to Expire in Some African Countries

With growing community transmission and high average mortality rates from the coronavirus in Malawi, there was widespread concern among the country’s health care advocates this week when the authorities announced that they would throw away 16,000 vaccine doses that had expired.

They were part of a total of 512,000 AstraZeneca vaccine doses that the landlocked southeast African nation had received from India, the African Union and Covax, the global initiative to procure and distribute vaccines. Health officials didn’t specify why the vaccines had expired, but said the doses went void on Tuesday “due to varying expiry dates of the received vaccine consignments.”

Health experts and campaigners warned that vaccine hesitancy, along with rumors that out-of-date jabs were being administered, might have contributed to the slow distribution of the vaccine doses and their eventual expiration.

In many African countries, vaccination campaigns have been hindered by factors like science skepticism, limited or no efforts to educate the public, inefficient distribution systems and concerns over the extremely rare but serious cases of blood clots being investigated among a small number of people who received the AstraZeneca and Johnson & Johnson vaccines. Those two vaccines, which require less stringent refrigeration, are crucial to efforts to immunize populations in poorer countries.

stopped plans to secure the AstraZeneca vaccine — a decision one official said was made to avoid duplicating the efforts of Covax, which will still supply AstraZeneca to African nations. But even though the decision was not linked to concerns over blood clotting, experts said it could still magnify misinformation about the vaccine. And the African Union is shifting its focus to the Johnson & Johnson vaccine, which could add to the problem. Its use has been paused in the United States.

In African countries, public confusion over whether to get inoculated, and if so when and where to do so, has contributed to the expiration of doses. Like Malawi, South Sudan saw 59,000 unused doses expire this month.

The problem is not unique to African countries. Tens of thousands of jabs have also been thrown away in countries like France and the United States. But African countries face far more serious supply shortages. According to a New York Times database, Africa has the slowest vaccination rate of any continent, with many countries yet to start mass vaccination campaigns.

Countries like Ghana, which was the first African nation to receive doses from Covax, is about to run out of its initial supplies with no sense of when the next batch may come.

“This inequality negatively affects the entire world,” said Dr. Ngozi Erondu, an infectious disease specialist and a senior health scholar at the O’Neill Institute at Georgetown University. If “entire regions and countries remain insufficiently vaccinated,” she said, “it will continue to ravage populations with persistent morbidity and leave the larger global health community always vulnerable to the virus.”

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