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At a cafe on 18th Street in San Francisco, David sipped coffee and talked about the regimen of daily HIV pills he recently started: Viread in July, and then last month, Isentress. He looked exhausted.

David does not have HIV. For 20 years he has endured a debilitating case of chronic fatigue syndrome, which has left him unable to work.

“All of a sudden my brain dies,” said David, who asked that only his first name be used for privacy reasons. “I have such a narrow range of concentration.” He hopes the medications will help.

Thirty years into the AIDS epidemic, the antiretroviral drugs that have provided lifesaving treatment for many of those infected with HIV — 1.1 million in the United States today — are now being used or considered for treating other ailments.

When medications have proved safe and effective for most patients, it is standard practice for pharmaceutical companies to see if the drugs have other applications. But with HIV drugs, the practice has been unusually contentious, fostering debates about questionable science, safety and profiteering, and concerns that thousands of Americans infected with HIV cannot get the medications.

At the center of this controversy is Gilead Sciences, a pharmaceutical company based in Foster City. Gilead is the nation’s largest producer of HIV medications (including Viread, Truvada, and Atripla), accounting for nearly half the United States market for them. The drugs produce $3.5 billion in annual revenues, with profit margins reportedly twice the industry average.

The Food and Drug Administration approved Viread to treat chronic hepatitis B in adults in 2008. And after a 2009 study linked chronic fatigue syndrome — a mysterious tiredness believed to afflict a million Americans — to a retrovirus called XMRV, there was hope that HIV drugs might also work against that ailment.

But that idea soured when other scientists could not reproduce the study’s results and concluded that the findings were incorrect. Science, the medical journal that published the research (conducted by the Whittemore Peterson Institute of Reno) has taken the unusual step of asking for a retraction. The institute declined to comment for this column.

Many doctors still believe that some type of virus, even if not XMRV, causes chronic fatigue, and an unknown number of patients continue to try HIV drugs as a treatment. With a doctor’s prescription, Dave said he received his medications from drug makers without charge, because of his low income.