The deaths and 15 other cases of illness were originally attributed to St Louis encephalitis, which causes fever and brain swelling and is the most common form of viral encephalitis in the US.
The virus is spread by mosquitoes so health officials have been spraying New York with insecticide to contain the outbreak.
However, researchers now say West Nile-type virus, previously only seen in Asia and Africa, could be behind some of the cases.
It is closely related to St Louis encephalitis and is carried by birds and spread to humans by mosquitoes which have bitten infected birds and then bite humans.
It cannot be passed from human to human or from birds to humans.
DNA sequencing
Experts from the Centres for Disease Control and Prevention (CDC) have said DNA sequencing of brain tissue on one of the dead confirms West Nile-type virus was to blame.
They are reviewing other cases as a result.
Barbara Reynolds, a spokeswoman for the CDC, said on Sunday: "CDC is continuing to look and retest some of our serology samples from patients in this outbreak to determine whether in fact they also have been infected with West Nile-type virus."
The CDC is also checking to see if the virus is similar to strains seen in other parts of the world or is a new variant.
Duane Gubler, director of the CDC's Division of Vector-Borne Infectious Diseases, said there was "considerable potential" for the virus to spread to Central and South America since infected birds could migrate.
Background Briefings
Medical notes
New York sprayed to control brain bug
(08 Sep 99 | Health)
Experts warn of brain fever epidemic
(04 Sep 98 | Health)
Encephalitis
Centers for Disease Control
World Health Organisation
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