Chronic fatigue syndrome, an illness that has long perplexed scientists, is not caused by a mouse virus, according to a federally funded study designed to end a bitter, long-running controversy on the issue.

The study, published online Tuesday by the scientific journal mBio, was headed by Columbia University’s Ian Lipkin, who led a team of scientists from different institutions — many of whom had published conflicting studies on the subject in the past.

The researchers said they could not find genetic traces of mouse virus in the blood of 147 chronic fatigue syndrome patients and 146 healthy people and therefore could not link viruses to the ailment.

Viruses became prime suspects for the disease — which afflicts more than one million patients in the U.S. and is characterized by extreme exhaustion not relieved by rest — in 2009, when Science magazine published a study by researchers led by Judy Mikovits, then at the Whittemore Peterson Institute in Reno, Nev. The study found traces of XMLV, a mouse retrovirus, in the blood of chronic fatigue syndrome patients.

A second study led by Harvey Alter, a scientist at the National Institutes of Health, and published in 2010, implicated a different, albeit related virus, pMLV. These findings raised hopes that researchers would be able to develop therapies to treat the illness.

But subsequent studies could not replicate those initial results. Last year, researchers reported that Mikovits’s samples of patients’ blood were most likely contaminated by mouse genetic material and that XMLV is apparently a virus strain that artificially arose in a laboratory in the 1990s — and so couldn’t be blamed for a disease first described in the 19th century.

In December 2011, Science magazine retracted the Mikovits study, after Mikovits herself refused to. Shortly afterward, the second team retracted its findings.

While at that point the majority of the researchers involved concluded that the mouse-virus theory had been debunked, some researchers, most notably Mikovits, continued to argue in favor of the virus theory. Mikovits was terminated by Whittemore in connection to the controversy.

But the debate is likely to end now, because the new study, in an unusual step, included Alter and Mikovits as collaborators and they agreed that no connection could be made between viruses and the disease. Both researchers were given blood samples independently and could not replicate their own findings from their initial studies.

“I applaud their courage,” said the study organizer Lipkin on Tuesday at a press conference that was attended by Alter and Mikovits. Lipkin speculated that the disease might be caused by several factors rather than a single agent, something that should be studied with modern methods. “It is simply not there,” said Mikovits of the suspected virus, “it is time to move forward now.”