The closures from 1:00 am to 5:00 am are aimed at eliminating traces of the potentially fatal virus from the subway's 6,500 wagons -- using every cleaning technique from basic sanitizer to ultra-violet lamps.
Epicenter of the pandemic
Authorities say conditions in New York -- the epicenter of the pandemic, with more than 19,000 confirmed or probable deaths -- are slowly improving, but that it's too soon to relax confinement measures.
For Gary Dennis, a New York tour guide in love with his city, its 424 subway stations and their gray carriages -- clunky and loud but as iconic as the Statue of Liberty or the bright yellow taxis -- the state of the transit system is a thermometer for the health of the metropolis.
'City would die without subway'
Dennis, a 59-year-old who lives on Manhattan's Upper West Side, said the city's decision to shutter service overnight left him "upset."
"This is a 24-hour town," he told AFP. "It's not designed to be empty, it's designed to be crowded."
"Without the subway, this town would die."
Mayor Bill de Blasio also describes the complex train system that snakes through the city as a "lifeline" that keeps New York's 8.6 million residents chugging along.
Since the pandemic hit the city, ridership has plummeted by more than 90 percent, according to the Metropolitan Transportation Authority that manages the network, to less than 500,000 passengers a day.
Normally some 5.5 million people take the subway every day.
Homeless people seeking overnight shelter
With many white-collar workers logging into the office from home, most riders are now "essential" workers -- some 800,000 employees of hospitals, supermarkets, repair personnel and delivery workers, many of them black or Latino, some undocumented migrants.
And controversy has grown over homeless people seeking overnight shelter in train cars. The city hopes closure will encourage them to find alternative shelter, but many advocacy groups have warned it will worsen the homeless crisis.
Giant vectors of this virus
Witnessing the deserted subway stations leaves Will Ramos, a plumber and handyman, mourning the loss of "culture within the stations."
"You meet a lot of talent down here," the 33-year-old said at the Union Square station, one of the network's largest.
But the pandemic has transformed the underground into "giant vectors of this virus," in the words of conductor Sujatha Gidla, who contracted the COVID-19 illness.
Transit authority could lose billions
In a scathing open letter published this week in The New York Times, Gidla denounced precautions taken to protect MTA workers as too little too late, saying "essential" staff were treated as "expendable."
According to the MTA's president Patrick Foye, 109 of 50,000 workers have died after contracting the virus.
The subway system -- much of it devastated by Superstorm Sandy in 2012 -- was already undergoing costly renovations, a project deemed urgent after years of negligence.
Now experts estimate the transit authority could lose $4-8 billion due to the pandemic.