Gilead Sciences and its breakthrough work in developing treatments for hepatitis C, the frequently devastating liver disease, have in recent months become the focal point of the debate about the cost and benefits of pharmaceutical products.

The biotechnology company introduced Sovaldi, a medication that when taken together with other drugs effectively cures hepatitis C in 90% of cases, shortly after it was approved by the Food and Drug Administration in December 2013.

The unprecedented efficacy of Sovaldi in treating the chronic disease garnered much attention in the health care community and beyond; so did its cost. With a price tag of $84,000 the 12-week course of treatment has met with growing resistance from third-party payers responsible for managing pharmacy benefits in both the public and private sectors. They express understandable concerns about what widespread use of Sovaldi could do to budgets, and many of them have started to restrict use of the medication to the sickest patients.

Gilead’s latest product is a medication that pairs sofosbuvir, the active ingredient in Sovaldi, and ledipasvir in a single pill that needs to be taken just once a day. Called Harvoni, the drug works by counteracting the enzymes needed for the virus to reproduce.

“With the development and approval of new treatments for hepatitis C virus, we are changing the treatment paradigm for Americans living with the disease,” Dr. Edward Cox, director of the office of antimicrobial products at the FDA’s Center for Drug Evaluation and Research, said when Harvoni was approved for marketing earlier this month. “Until last year the only available treatments for hepatitis C virus required administration with interferon and ribavirin. Now patients and health care professionals have multiple treatment options, including a combination pill to help simplify treatment ­regimens.”

By combining everything needed to treat the disease in one pill and reducing the number of doses required to one a day, Gilead has significantly increased the chances that patients will adhere to the medication regimen and thus raise an already remarkable cure rate.

Once again, the only major drawback appears to be price. A 12-week course of treatment with Harvoni, which is typical for hepatitis C patients, will cost $94,500. Pharmacy benefits managers are sure to voice the same concerns about Gilead’s new medication as they did about Sovaldi.

The Harvoni/Sovaldi conundrum can be viewed from multiple perspectives, with the outcome of the cost-benefit analysis shaped by where one stands in the health care continuum.

Information provided by Avella Specialty Pharmacy helps put the issue in perspective. Three million people in the United States now have hepatitis C, although more than three-quarters of them are unaware that they do, and that number is expected to grow fourfold during the next two decades. The cost of helping such patients is high, with the most expensive form of treatment, a liver transplant, coming in at more than $500,000. Individuals who undergo such surgery must take medication for the rest of their life to prevent rejection of the transplanted organ, and even then 28% of them die in less than five years.

In light of the tremendous expenditures involved in the most severe cases and the substantial costs related to more routine treatment of hepatitis C, a process that goes on for a lifetime, there is a strong case for using medications — even extremely expensive ones — to cure the disease in its early stages. Savings would accrue over the long term and the quality of life for patients would be improved immeasurably.

The structure of the health care system itself stands in the way of a holistic approach. Incentives between providers and payers are too often misaligned. In the case of a drug like Harvoni, the first inclination of physicians and pharmacists would be to put patients on the medication if they think it is the best option to improve their health. For third-party payers, cost is a factor that can weigh as heavily as patient outcomes.

The only way to ensure that the health care system does what is best for the patient is to work toward greater harmonization of the incentives that motivate providers and payers.