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A federal program to immunize the country’s youngest children against a wide range of diseases will begin next year, taking a step that advocates say is long overdue, but one that critics say will prove monumentally expensive.

The initiative, which Congress approved last summer, will provide free vaccine to millions of poor and uninsured children. Public health officials hope that the new entitlement program will bolster the nation’s low immunization rate for children younger than 5. About 11 million children will be eligible under the act.

“The goal of public health is the prevention of disease,” said D.A. Henderson, deputy assistant secretary for Health and Human Services and an architect of the program. “Of all the medical procedures we do today, immunization is one of the most cost-effective ways of fulfilling that mission.”

Children’s advocacy groups argue that not vaccinating the young could lead to epidemics, while pharmaceutical companies that manufacture the vaccines say that selling to the government on a massive scale will lower profits and discourage research.

Both sides agree that many children now go without their recommended shots. Many health insurers don’t cover the cost of vaccine, which has soared in recent years. Preschool children need 18 doses of vaccine administered in seven sessions to be fully immunized. At market rates, the series costs about $244.

“Immunization is probably one of the most expensive health-care expenses associated with young children,” said Carol Regan, representative for the Children’s Defense Fund, which supports universal immunization. “In 1977, full regime cost $11. Now, the cost exceeds $230.”

The Children’s Defense Fund estimates that nearly half of the country’s 2-year-olds haven’t been fully immunized, which the group blames on cost and a poor system for getting the vaccine to the children.

Last spring, the Clinton administration proposed that the federal government purchase and distribute all childhood vaccines without cost. Congress refused to go along with that, but it did allow the states to buy vaccines at deeply discounted prices from the federal government, and at least 15 states are likely to subscribe.

Congress is considering companion legislation that would improve the way health agencies deliver vaccines. Measures under consideration would create a computerized tracking system to monitor the shots children have received, would expand health clinic hours and would pay for programs to educate parents on the need for vaccinations.

“There is strong bipartisan support to address these three remaining areas,” said Jackie Noyes, director of the American

Academy of Pediatrics. “It’s like we had a car with four flat tires. We fixed one tire with the vaccination legislation, now we’re about to repair the other three flats.”

The four pharmaceutical companies that manufacture vaccines in the United States remain skeptical about the new system. They envision falling profits and suggest that unless it can do a better job of reaching the unvaccinated public, the program will be ineffective.

“What Congress passed is a multibillion dollar entitlement program that assumes that price has been the factor inhibiting parents from vaccinating their children,” said Isabelle Claxton, a Washington lobbyist for Merck & Co., one of the vaccine manufacturers. “Everyone wants to increase the level of immunization in this country, but we believe a lack of outreach is the real problem.”

Claxton said the immunization program could cost the federal government more than $500 million annually over the next five years. Since the drug companies sell vaccines to the government at a lower price than to private physicians, they say that an expanded federal program will cut profits and money for research.

“This legislation has the potential of eliminating the private market,” Claxton said.

“The companies need a private market to afford a discount in prices for vaccine for the poor. Much more vaccine will now be sold at the public price. Unfortunately, we will have to weigh our commitment to long-term public health against our commitment to our shareholders.”

Governments now buy about 55 percent of the output of Merck and the other vaccine manufacturers. Claxton said the public portion might jump to 75 percent under the new program, which will take effect in October 1994.

Noyes sees it differently. She says the two-price system has contributed to the skyrocketing cost of vaccines.

“Middle-class families are subsidizing low-income families who receive free vaccine,” Noyes said. “They pay higher prices than the government pays for the same product, and they pay for the government purchases with their taxes.”

Noyes said immunization reform was a first step toward an overhaul of the national health care system.

“This was the curtain-raiser for health-care reform,” she said. “Really, I’m aghast that it became a topic of debate. If children become infected with preventable diseases, the whole community will pay for a lifetime of treatments that will cost much more than a series of vaccinations.”

The vaccine delivery system could change again under President Clinton’s health-care reform proposal. In that plan, all insurers would be required to provide vaccination without co-payments as part of a basic package. Effectively, every child then would have access to vaccine.

Kay Johnson, policy director for the March of Dimes, a charitable foundation that funds research into and treatment of birth defects, said that this year’s debate over vaccination could set the tone for Congress when it grapples with health care.

“The questions raised during the immunization fight go to the heart of the health-care debate,” Johnson said. “Congress asked how far government should go, and how it could negotiate new relations with industry for the delivery of products and services.”

Every Child By Two, a group founded by former First Lady Rosalyn Carter and Betty Bumpers, wife of Sen. Dale Bumpers (D-Ark.), is taking the cause of immunization to communities around the country. Its goal is to immunize all children under age 2 through either national or local efforts.