Other times the subway system shut down in the past: The hours following the September 11, 2001, attacks, and a hand full of times when extreme weather conditions arose - like during hurricanes Irene (2011) and Sandy (2012), and the blizzard of 2015. This is the first deliberate shut down.
To adjust to the loss of subway transit, the MTA will be adding hundreds of overnight bus lines for the 11,000 estimated passengers that use the trains at night.
The initial 24-hour closure was intended to give MTA workers the chance to clean the cars and structure more effectively, as well as to give the NYPD enough time to remove the estimated 2,200 homeless people who use trains and station in the underground system as shelter each night.
Police and outreach workers will handle the homeless people who have been sleeping on the subway - which has run around the clock for more than a century - said New York Governor Andrew Cuomo at a weekend briefing, offering to get them services and shelter.
"You do not help the homeless by letting them sleep on a subway car in the middle of a global pandemic," Cuomo said. "I think it's actually an opportunity to get them off the trains and actually connect them to the services they've needed."
The MTA itself has lost 109 worker to COVID-19, the disease caused by the coronavirus that originated in a wet market located in Wuhan, China. This is the most of any New York state-run agency, according to NPR.
"Extraordinary times call for extraordinary measures," MTA chairman Patrick Foye said the night before the deep-cleaning, according to CNN. "This is critical to ensure the health and safety of our employees and customers."
Cuomo said that after the day-long deep-cleaning, the subway system would be closed each night between 1 and 5 a.m. beginning May 6, to allow the MTA to disinfect the cars each night to prevent further spread of the novel coronavirus."This is a daunting challenge," Cuomo said at a daily briefing last week. "The entire public transport system in downstate New York will be disinfected every 24 hours."
Worries have surfaced that these plans to close New York City's subways at night risk pushing hundreds of homeless people "further into the shadows," according to housing experts, calling for safe alternatives to house them.
Most city-run shelters or other shared housing options fail to protect the homeless from the deadly respiratory virus, housing activists said, with little space to self-isolate and often unsanitary conditions.
Health experts say homeless people are more likely to contract illnesses such as the coronavirus, in part because of weakened immune systems due to additional stress, and lack of nutrition and sleep.
More than 60 coronavirus victims have died in New York City homeless shelters, according to officials.
Shelters have been staggering meal times and have ended group activities, said Jacquelyn Simone, a policy analyst at the Coalition for the Homeless advocacy group, but the layout of shared housing does not lend itself to homeless people's need to self-isolate and practice social distancing like everyone else.
"Offering someone to return to a place with shared dorms, shared bathrooms and shared eating facilities is not actually meeting people's needs," said Simone.
The city has more than 100,000 vacant hotel rooms, by some estimates, that could be put to use instead, she said.
New York City has been America's epicenter in the pandemic, with more than 174,000 coronavirus cases and more than 14,000 deaths, according to its Health Department.
Reuters contributed to this report.