MAIDUGURI, Nigeria — An emergency polio vaccination campaign aimed at reaching 25 million children this year has begun in parts of Nigeria newly freed from Boko Haram Islamic extremists, with fears that many more cases of the crippling disease will likely be found.

Two toddlers discovered last month were Nigeria’s first reported polio cases in more than two years, putting the world on alert just months after the African continent was declared free of the disease.

One member of the Rotary Club’s “End Polio Now” drive said he almost cried when he got the news. It was a major blow to global efforts to stamp out polio, which persists in only two other countries, Pakistan and Afghanistan.

The Associated Press joined the vaccination drive in northeastern Nigeria, a campaign going to extraordinary lengths to fight the disease in areas still threatened by Boko Haram extremists who violently oppose Western medicine.

Health workers using military helicopters, all-terrain vehicles and even tricycle taxis vaccinated about 1.5 million children in the past week alone, starting in the refugee camps where the new cases surfaced.

The World Health Organization has said the two new cases indicate the wild polio virus has been circulating for five years in northeastern Borno state, where Boko Haram began its uprising in 2009.

MORE CASES EXPECTED

More cases are expected to surface as Nigeria’s military forces Boko Haram out of more towns and villages, said Dr. Tunji Funsho, head of Rotary’s polio eradication drive.

Just 20 years ago, this West African nation was considered the world’s epicenter of polio, recording 1,000 cases a year. Men and women with twisted limbs crawling along the roadside to beg are still a common sight. A global drive to end polio began in 1988, when the highly contagious disease was endemic in 125 countries.

Though progress has been made, wiping out polio probably will not be possible without ending the unrest tied to Islamic extremism that prevents vaccination in the three countries where the virus still is endemic, according to a new report from U.S.-based risk analysis group Stratfor.

“Boko Haram is largely responsible for the insecurity that has hamstrung vaccination efforts in Nigeria,” the report said. “Though the group has weakened since the start of 2015 … as long as this security risk remains, so, too, will the risk that Nigeria’s latest run-in with polio will not be its last.”

Boko Haram is in retreat but remains deadly. In July, militants attacked a humanitarian convoy near Maiduguri, the region’s largest city, leading the United Nations to suspend aid to newly liberated areas where it says half a million people are starving.

Boko Haram’s opposition to all things Western reached new heights in 2013 when militants shot and killed nine women vaccinating children against polio in northern Kano, Nigeria’s second largest city.

Over the years, the vaccination campaign has had to fight rumors that the vaccine was a plot to sterilize Muslims, which it overcame by winning over religious and traditional leaders and grassroots women’s groups.

‘A MAJOR SETBACK’

“Yes, it’s a major setback, but we are not defeatist,” Funsho declared of the latest cases. He looked over a map of Borno state that showed only a small southern section as “accessible,” most of the sprawling state “partially accessible” and a band in the north bordering Niger, Cameroon and Chad as “inaccessible” because of Boko Haram fighters.

Over the past week, hundreds of health workers from the government, the United Nations and aid organizations spread out across Borno state, delivering the vaccinations through drops on the tongue.

It doesn’t end there. The polio vaccine has to be administered at least three times to each child, and up to five times in endemic areas, so more rounds are planned next year.