Four months later, that's still a mystery.
And experts aren't so sure about stories of hordes of displaced rodents fleeing the flood zone and taking up residence in buildings that were previously rat-free.
TV stations and newspapers have been rife with reports about rats infesting parked cars and fleeing the East River waterfront for the brownstones of Brooklyn Heights and exterminators enjoying a boom in business.
For some city officials, the last straw came a week ago when a rodent problem forced a two-day closure of Magnolia Bakery, a Manhattan landmark often credited with starting a national cupcake craze. Within days, a city councilwoman floated a proposal to create a $500,000 emergency rat mitigation program for storm-impacted neighborhoods.
But the city's health department, which collects reams of data about the rat population and maps infestations looking for trends, said rodent complaints actually had declined since the late October storm, which was spawned when Hurricane Sandy merged with two other weather systems.
"The Health Department conducted extensive inspections in flood zones after Hurricane Sandy, provided guidance to home owners and baited the area. But we did not see an increase in the rat population," the agency said in a statement. "Large storms can flush out rats, but they also drown many rats, and the net effect of large storms is often a decrease in the rat population."
The number of rodent-related citations issued by health inspectors has dropped as well.
The Metropolitan Transportation Authority, which runs the city's subway system, the nation's largest, also dismissed tales of rats being stirred up by Sandy.
"We noticed no unusual rat activity or rodent activity in the wake of the storm," agency spokesman Charles Seaton said.
He also said that when water was pumped out of flooded tunnels and stations, there weren't large numbers of rat carcasses left behind.
The idea of a mass rat migration drew ridicule from Richard Reynolds, who leads a group of dog owners who conduct urban rat hunts.
"What happened to the rats? Nothing! We're finding rats right where we've always found them," he said. "I think this whole idea that there has been some kind of major relocation of rats is just good news media fodder."
He noted, as did other experts, that Norwegian rats, the species found in New York, are known for being especially strong swimmers.
"I have seen them dive over 70 feet, swim 500 yards, give me the finger and head for the hills," he said. "Hurricane Sandy is not going to affect these critters."
Hard scientific data, though, is still largely lacking, and there is plenty of room for debate.
Retired pest control expert Dale Kaukeinen, who spent 30 years in the extermination business, said his first instinct was that Sandy probably decimated the rodent population in some neighborhoods. But he said he couldn't rule out the possibility that displaced rats had moved into new territory.
"They are adaptable. They can swim. They can move distances," he said, citing radio telemetry studies showing that rats can move several miles if displaced by environmental conditions.
Also, because rats live in a world of smell, their former homes might have been rendered unfamiliar by a flood, he said, even if the buildings, parks or tunnels they had been living in suffered little permanent damage.
"To a rat, it wouldn't look the same, it wouldn't smell the same," he said.
Jessica Lappin, the councilwoman who proposed the emergency extermination program for flood-damaged neighborhoods, said she was skeptical when she first started hearing stories about rat infestations since the storm but has come to believe the problem is real.
"We are used to seeing rats. But it definitely seemed to be getting worse," Lappin said.
She noted that even though the health department's citywide rat complaint numbers show no increase, there has been a rise in select Manhattan neighborhoods near where flooding occurred.
Those neighborhoods include the West Village, where mice first turned up in a basement storage area at Magnolia Bakery in the weeks after the storm, company spokeswoman Sara Gramling said Thursday. The bakery was cited by city health inspectors in January, then was closed down Feb. 14 after a follow-up inspection. It reopened two days later, with lines even longer than usual.
Gramling said she was sure the storm was a factor in the infestation, although she noted that there is also a large construction project taking place down the block.
"At the building, and in the West Village, there has been an influx across the board," she said. "We don't feel like it's an isolated incident. Clearly there is a trend."
Thomas King, a manager at M&M Pest Control, an extermination business based in Chinatown, said his company's rat calls are up 20 percent to 30 percent since the storm.
Recent media coverage of the supposed rat scamper caused by Sandy has focused on Brooklyn Heights, a historic district perched on a hill above the East River. But the neighborhood's rat problem is hardly new. Nearly every year has brought a new newspaper story about rats in the neighborhood, usually linked to trash left by visitors to the Brooklyn Promenade, the neighborhood's elevated esplanade.
The Brooklyn Heights Association, a civic group, did get some reports after the storm about new rat burrows being dug in gardens along the Promenade, but city park officials took quick action, and there have not been any complaints since.
So the mystery remains.
At least one notable rat population perished for sure: 7,000 lab rats and mice at a New York University research facility died when the building flooded during the storm.
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