The encephalitis virus has been found as far as 150 miles north of the city.
But state Health Department officials say the risk of upstate residents contracting the virus is minimal.
The virus, which is carried by mosquitoes, was found in a dead crow collected earlier this month in the village of Ballston Spa, 150 miles north of Manhattan.
It was also discovered in a deceased cuckoo found at the U.S. Military Academy at West Point, 40 miles north of the city. No human encephalitis cases have been reported upstate.
But officials urged residents to take precautions against mosquito bites until freezing weather further inactivates the pesky bug.
Finding birds with the virus upstate doesn’t mean the encephalitis outbreak is spreading broadly, said Health Department spokesman John Signor. The birds may have become disoriented because of the virus and flown north instead of south, he said.
The encephalitis virus has killed six people and infected 55 others in the New York City area.