The AIDS virus hides out inside people’s intestines, researchers said on Saturday in a report that offers new understanding of the incurable infection.

The virus replicates in the lining of the gut and does much of its damage to the immune system there, Satya Dandekar, chairwoman of the Department of Medical Microbiology and Immunology at the University of California Davis Health System, and colleagues reported.

Writing in the Journal of Virology, Dandekar said the study was the first to explain why the drug cocktails taken by HIV patients so often fail to work completely.

“The real battle between the virus and exposed individuals is happening in the gut immediately after viral infection,” she said in a statement.

“We need to be focusing our efforts on improving treatment of gut mucosa, where massive destruction of immune cells is occurring. Gut-associated lymphoid tissue accounts for 70 percent of the body’s immune system. Restoring its function is crucial to ridding the body of the virus.”

HIV cannot be cured but the drugs, known as highly active antiretroviral therapy, or HAART, can keep the virus under control.

At first, doctors had hoped that years of treatment might eventually eradicate the virus, but, 25 years into the epidemic of AIDS, it is clear that cannot happen. That is because the virus can hide out quietly in reservoirs, which include certain immune cells.

The gut is clearly important, too, Dandekar’s team said.

“We found a substantial delay in the time that it takes to restore the gut mucosal immune system in those with chronic infections,” Dandekar said. “In these patients the gut is acting as a viral reservoir that keeps us from ridding patients of the virus.”

The mucosa are the wet tissues that line the nose and throat, the genitals and the inside of the gut. HIV often infects people via the mucosa.

Dandekar’s team has been studying HIV-infected patients who, even without treatment, have survived more than 10 years with healthy immune systems, including the T-cells that are attacked by the virus.

“We looked at their gut lymphoid tissue and did not see loss of T-cells there. This correlated with better clinical outcomes,” Dandekar said.

So they started the current study, following 10 patients being treated with HAART, taking blood and gut samples before and after three years of treatment.

They found evidence of inflammation, which disrupts tissue function, promotes cell death and upsets the normal balance of gut bacteria.

Dandekar said these findings suggest anti-inflammatory drugs may help HAART work better.