Heavy rain on Thursday swamped areas of the US northeast already sodden from Hurricane Irene, with up to five people killed as flash floods forced over 100,000 to leave their homes.

The National Weather Service (NWS) issued a flash flood warning for counties in New York, New Jersey, Pennsylvania, Connecticut, Maryland and Virginia, as towns became inundated, busy highways closed down and commuter lines backed up.

US President Barack Obama declared an emergency in New York state, ordering federal agencies to coordinate disaster relief efforts to "save lives and to protect property and public health and safety," the White House said.

Some 100,000 people in Pennsylvania's Luzerne county are under "mandatory evacuation" orders, including 20,000 in the city of Wilkes-Barre, according to local officials.

Stephen Bekenich, the county's emergency management director, warned that those who remained in flood-prone areas could not count on being rescued.

"If folks choose not to leave, they are taking (their) lives into their own hands," he said. "Help may not be able to reach them."

The city of Binghamton, New York -- where 8.5 inches (21.6 centimeters) of rain fell in 24 hours -- ordered a mandatory city-wide evacuation, affecting 10,000 people.

Flooding was also reported in and around the US capital Washington.

"We expect historic or near-historic flooding in many parts of the state," Pennsylvania Emergency Management Agency spokeswoman Ruth Miller told AFP.

Three unconfirmed fatalities during the stormy weather have been reported to authorities in Pennsylvania, she said, as the state grappled with some of its worst flooding since 1972's benchmark Hurricane Agnes, which ravaged much of the mid-Atlantic region as a deadly tropical storm.

"It's bad now, and there are some places where it will get worse," Miller said. "There is more rain that continues to come down (and) we don't expect this to end for quite some time."

Two people, one of them a young boy who was swept away in a river, died in northern Virginia, a spokesman for the Fairfax County Fire and Rescue Department said.

New York Governor Andrew Cuomo, who had earlier mobilized emergency response resources, also warned of further severe flooding, calling the situation "frightening."

More potentially dangerous weather is expected in the northeast after Irene, which was blamed for more than 40 deaths.

Three cyclones are brewing in the Atlantic: Tropical Storm Nate, hovering in the Gulf of Mexico and threatening Mexico and Texas; fast-moving Tropical Storm Maria, which could hit Puerto Rico early Sunday and the Bahamas next week; and Hurricane Katia, off the US east coast and expected to remain out at sea.

The latest foul weather is the remains of Tropical Storm Lee, which slammed into the Gulf Coast on Sunday, dumping torrential rains on a huge swath of the American south, mid-Atlantic region and northeast already drenched by Irene.

"It is a double-whammy," said spokesman Bill Peat of the New York state Office of Emergency Management.

Irene dumped more than 12 inches (30 centimeters) of rain in parts of New York and Pennsylvania over the past four days, triggering huge floods.

National Guard troops have been deployed in New York and Pennsylvania, and rescue personnel are on standby.

The flash flood warnings include much of New Jersey, which suffered devastating flooding from Irene after it made landfall hundreds of miles (kilometers) south and trailed heavy rains all the way up the coast.

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