The trains, which had been running on a reduced schedule since late March, are now going to be stopped from 1 a.m. to 5 a.m. each day.
Most stations don't even have a gate, meaning there's no way to physically lock them. So more than 1,000 officers have to stand watch overnight at close to 300 stations.
Inside the 96th Street Q train station, MTA workers disinfected trains as they did at all 472 subway stations overnight. They're also cleaning trains parked at the yards and cleaning throughout the day.
"We will be tracking each individual train car that we are cleaning in each of the three different formats so that we'll be able to track them over a 24 hour basis," Vice President of Subways Sally Libera said. "And we expect that many of the cars of our fleet will actually be cleaned and disinfected more frequently than ever 24 hours."
For the first time, every single homeless person is being escorted out of the subway system before the cleaning begins.
At 29 terminus stations, homeless advocates are providing services to the people being moved off the trains.
New York City normally has the country's busiest public transit system, with a weekday ridership of more than 5 million.
Ridership has fallen 92 percent since the pandemic began, but this cleaning is about keeping essential workers safe including MTA employees. Officials said 109 have died so far.
The MTA says overnight service will resume when customer demand returns, and "innovative and efficient disinfecting techniques have been successfully deployed systemwide."
Buses are free during the shutdown period, though officials said they are looking at increasing that service after ridership numbers were higher than expected the first night.
"I think we may want to look at tweaking bus service a little bit," interim NYC Transit President Sarah Feinberg said. "We had thousands of people on buses last night, more than we normally have in an overnight service. That means people took us up on our increased and enhance bus service, which is great news."
She said ridership increased 60%
More information is available from the MTA at new.mta.info/coronavirus/overnight.
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