The case raised hopes that more of the roughly 250,000 children who are born each year infected with the human immunodeficiency virus, which causes AIDS, might have a shot at a cure.
Those hopes were dashed when the child's doctors discovered last week that the HIV virus had begun replicating, Dr Anthony Fauci, director of the National Institute of Allergy and Infections Diseases, said at a press conference on Thursday.
"Certainly, this is a disappointing turn of events for this young child, the medical staff involved in the child's care and the HIV/AIDS research community," Fauci said in a statement.
The girl, now 4, was born prematurely in a Mississippi clinic in 2010 to an HIV-infected mother who had received no prenatal care.
After her birth, the child was rushed to the University of Mississippi Medical Center, where Dr Hannah Gay, a pediatric HIV specialist, decided to take aggressive action, offering the newborn a three-drug cocktail of powerful HIV medications. Normally, children suspected of HIV infection are given a milder course of treatments until tests can confirm the infection.
The child remained on treatment for 18 months, then stopped coming in for treatment. When she returned to the medical center some weeks later, the child showed no sign of the virus.
Since March, the child's progress has been monitored closely, and until last week, she had gone 27 months without treatment. Tests during that time showed no evidence of the virus.
That changed during a scheduled check-up last week, in which doctors discovered the virus had begun to replicate. The girl is now being treated with anti-HIV drugs, treatments she will likely need to take for the rest of her life unless a cure can be found.
Gay described her disappointment as "a punch to the gut."
The developments likely cast doubt about the prospects of a cure for an HIV-infected California baby. In March, that child's doctors announced they had used the same approach and have found no trace of virus in the baby after nine months of treatment. Because that child is still being treated, however, the case was not classified as a cure.
Even so, Fauci said the Mississippi case remains important because it confirms that the baby was indeed infected, something that had been doubted, and that early and aggressive treatment helped prevent the virus from replicating.
Fauci in May had announced plans to study more children using that same technique, but he will be taking a "hard look" at the design of that study now.