The Mississippi girl born with HIV who was believed to be cured after aggressive early treatment has tested positive for the virus, a disappointing setback for HIV/AIDS research.

The child, who had not been on antiretroviral therapy for 27 months, was believed to be the first person to have the virus completely eliminated through drugs, and scientists had hoped to be able to replicate her regimen to treat other babies infected at birth.

“It felt very much like a punch to the gut,” Hannah Gay, a physician who treated the baby, said during a news conference Thursday.

The child, whose name has not been revealed, was at high risk for infection because her mother was HIV-positive and had not received any treatment during pregnancy. Doctors typically do not treat infants with the drugs until at least six weeks after birth when they can be certain the babies are infected.

But in a highly unusual move, doctors at the University of Mississippi Medical Center in Jackson began administering an aggressive triple-drug treatment 30 hours after the baby was born prematurely in 2010.

1 of 35 Full Screen Autoplay Close Skip Ad × A look at the history of AIDS in the U.S. View Photos Robert Gallo and Luc Montagnier identified HIV — the virus that causes AIDS — in 1983. The three decades since have seen wide medical and cultural advancements in our understanding of the virus. The years have also brought much hardship and controversy. Here’s a photographic history of the AIDS epidemic in the United States. Caption A photographic history of some of the defining moments of the AIDS epidemic in this country. December 1985 This image shows a magnified view of the AIDS virus taken by researchers in the medical department of Tokyo’s Tottori University. The photo, magnified 350,000 times, was taken with a scanning electron microscope. Researchers said the virus of the deadly disease has a rugged surface. Nearly 30 million people have died of AIDS since the first five cases were recognized in Los Angeles in 1981. About 34 million people have HIV now, including more than 1 million in the United States. Tottori University via AP/Kyodo News Buy Photo Wait 1 second to continue.

The virus in the infant’s blood declined steadily over time, and 29 days after birth it was undetectable. The baby received treatment until about 18 months of age. But the treatment ended when the mother stopped bringing the child to the appointments and doctors were unable to locate her.

The mother and child showed up five months later, however, and researchers were surprised to find there was no detectable virus despite the fact the child had not received any treatment during that time.

Given the lack of any measurable signs of infection, doctors decided not to restart the anti-retrovirals. During subsequent visits, spaced out every six to eight weeks, the child continued to test negative for the virus.

When the details of the case were presented in March 2013 at a medical conference and later published in the New England Journal of Medicine, hopes were raised that a cure had been found for the estimated 260,000 babies born with the virus around the world each year.

Gay said the child came again this past week and appeared physically well. But a few days later the blood work came back and showed signs of the virus.

Anthony Fauci of the National Institutes of Health and other doctors involved in the girl’s treatment called the results “very disappointing” but said that scientists had learned a lot from the case.

The girl, who is 3 years 10 months old, is now back on antiretroviral treatment and is responding well, doctors said.

Researchers confirmed through DNA sequencing that the infection in the child is not a new infection but was the one passed from the mother.

“We knew it was a possibility. . . . We had no way to predict if and when that might occur,” Gay said.

Gay said the child this past week received three antiretrovirals on the same evening that HIV was detected in her body. Three days after treatment, her viral load had fallen from 16,750 copies per milliliter of blood to 2,658 copies per milliliter — which shows a positive response to the treatment.

A baby in Los Angeles who was also born with the virus was treated with a similar regimen a few hours after birth. Tests revealed that the baby seemed to have completely cleared the virus and not just suppressed it. The case, revealed in March, appeared to confirm the idea of a cure. Researchers said Thursday that that baby was never taken off antiretrovirals and remains free of the virus.

Deborah Persaud, a professor of infectious diseases at Johns Hopkins Children’s Center who was involved in the treatment of the second baby, suggested that the outcome, while not a cure, was still a major step forward. She said the evidence so far clearly supports the idea that early treatment can help keep the virus at bay.

“This duration of time frame off antiviral treatment of 27 months is really unprecedented for perinatal HIV infection,” she said.

The researchers said that they are still very much in the discovery phase, and that it’s too soon to make any recommendations for treatment based on the news.

Scientists’ search for a cure for HIV has led to many false starts. The first and perhaps only adult believed to have been cured of an infection is a man known as the Berlin patient, whose blood cells were treated with powerful radiation and chemotherapy, and who underwent a bone-marrow transplant from a person who had a rare resistance to HIV.

The Mississippi case had been seen as so promising that the NIH in June launched a global study to try to replicate the results in 54 infants. In the United States, mother-to-child transmission is rare because mothers are routinely treated with antiretrovirals during pregnancy, reducing the possibility of infection to close to 1 percent. But the problem is more acute in parts of the developing world, especially in rural areas where medical treatment is difficult to access. The plan was to treat the babies within 48 hours of birth, and if they continue to be virus-free for an extended period (two years was discussed as a possibility) they would be taken off the therapy.

Fauci, the director of the National Institute of Allergy and Infectious Diseases at the NIH, said Thursday that the study will continue but that no children had been enrolled yet and that researchers would have to reevaluate the parameters of the research, given the news.

He said that many questions remain about what happened to the Mississippi girl. The most intriguing may be regarding how a reservoir of HIV could hide in the child without being detected by even the most sophisticated tests used by the researchers.

How can someone be off therapy for 27 months with no detectable immunological response to the virus and yet the virus remain suppressed? Fauci asked. If it was not an immune response suppressing the virus that we could measure, then what was keeping the virus from rebounding? Were there defective viruses present that over time became active? If so, what triggered that? From what cell or body compartment did it come from?

“We have a situation that is obviously disappointing,” Fauci said. “But nonetheless there are certainly many confounding issues that arise and that will trigger intense discussion and further study.”