New York Governor Andrew Cuomo made the announcement during his Monday briefing, saying the patient was transferred from Connecticut to the NYC hospital.
Officials say there is no evidence of any spread in New York state to date.
"The South African variant they worry about how lethal it is and how it relates to the vaccine," Cuomo said.
The Connecticut state health department confirmed the positive case in a statement.
"Governor Lamont and state public health officials today announced that the B.1.351 variant of the COVID-19 virus, the so-called "South African" variant, has been detected in a Connecticut patient who is currently hospitalized out of state with the virus. The individual's condition is improving. This is the first known case of the B.1.351 variant in a Connecticut resident."
Meanwhile, officials say 3.2 million have received their vaccinations statewide and over 1 million New Yorkers.
The statewide positivity rate is 3.53%.
Long Island continues to have the highest positivity of the regions at 4.62%, while Mid-Hudson has the second highest at 4.53%.
Bronx continues to have the highest positivity in NYC at 6.11%.
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