They found that inflammation of the gut interfered with the action of highly active antiretroviral therapy (HAART), allowing a reservoir of HIV to build up in the gut and preventing the virus from being eradicated.
The study included 10 HIV patients, three of whom were treated with HAART within six weeks of infection and seven of whom did not receive treatment until the infection was already firmly established.
The researchers took GI biopsies and peripheral blood samples from the patients when they initiated treatment and again three years later.
They analysed the samples to establish their viral load and T-cell count.
They found that patients who did not start HAART until later stages of HIV had more active HIV in their gut tissue than the patients who initiated therapy in the early stages of infection.
The gut biopsies also had lower T-cell counts than the blood samples in both treatment groups, showing that the immune system was not recovering as quickly following HAART as would have been believed based on blood samples alone.
The researchers also found that inflammation of the gut was linked to slower T-cell restoration and increased viral load.
Lead researcher Dr Satya Dandekar, chair of the department of medical microbiology and immunology at the University of California Davis, said: 'We need to be focusing our efforts on improving treatment of gut mucosa.
'Gut-associated lymphoid tissue accounts for 70 per cent of the body's immune system. Restoring its function is crucial to ridding the body of the virus.
'While current HIV therapy is quite successful in reducing viral loads and increasing T-cells in peripheral blood, it is not so effective in gut mucosa.'
Journal of Virology. 2006; 80: 8,236-47