The Centers for Disease Control and Prevention (CDC) said tests indicated that the outbreak of 31 confirmed and 25 probable cases was due to West Nile Virus, not a related or new strain.
"CDC has completed its laboratory work to confirm that this is West Nile Virus," spokeswoman Barbara Reynolds said in an interview. The CDC had earlier described the virus as "West Nile-like."
"We've confirmed through a number of tests that what we have here is the first introduction of West Nile Virus in the Western Hemisphere," Reynolds said.
Some researchers had suggested that the deaths and illnesses, initially diagnosed as St. Louis encephalitis, were instead caused by the Kunjin virus found in Australia and South America.
The CDC said that the New York encephalitis outbreak has waned because of mosquito-control efforts and cooler temperatures. The last of the 56 encephalitis cases developed on Sept. 22, the agency said.
"We do believe that this outbreak is waning and that's due to effective control measures, spraying for mosquitoes and the cooler weather," Reynolds said.
Thirteen people in New Jersey who were tested do not have the disease, state officials added.
"However, there are still a number of unanswered questions and the investigation continues," she said.
Researchers are testing birds along the Eastern seaboard to see if they are infected with the West Nile Virus. The CDC earlier said it found the virus in crows, domestic birds and exotic pet birds in New York, Connecticut and New Jersey. The virus also has killed one horse in New York.
"What we're trying to determine is what will this mean for New York residents in the area next spring. We're looking at what measures need to be put into place," Reynolds said.
"We'll be meeting with experts in a number of fields to determine what surveillance needs to be done between now and next spring and what other control measures may be needed to reduce the likelihood of this virus reappearing as a human outbreak next year," she said.
The West Nile Virus is commonly found in Africa, West Asia and the Middle East, the CDC said. It is not transmitted from person-to-person, but is spread from birds to mosquitoes to humans. The West Nile, Kunjin and St. Louis encephalitis viruses all belong to the same subgroup.
Encephalitis is an inflammation of the brain that can be caused by viral and bacterial infections. It is fatal in 3 to 15 percent of cases, with higher mortality rates among elderly people, researchers said.
Despite the lack of new cases, the CDC said people should continue to wear clothing such as long sleeve shirts and pants o reduce their contact with mosquitoes and should spray their clothing and exposed skin with insect repellent if they are outside at dusk and at night.
New York City health officials sprayed the entire city of 7 million people with insecticide in early September to try and kill off mosquitoes.