There is little evidence that the New York Subway is spreading the coronavirus, according to analysis by Alon Levy.

Alon Levy writes a rebuttal to arguments about the role of the New York Subway in spreading the coronavirus, especially a paper by MIT economist Jeffrey Harris, "claiming that the subways did in fact seed the Covid-19 epidemic in New York." According to Levy, however, Harris cites no evidence in building this argument, and so Levy debunks the paper.
After considering the low infection rates in other high-transit cities worldwide, Levy returns the focus to New York City:
So the question is not whether rapid transit systems are inherently unsafe for riders, which they are not. It’s whether New York, with all of its repeated failings killing tens of workers from exposure to the virus, has an unsafe rapid transit system. Nonetheless, the answer appears to be negative: no evidence exists that the subway is leading to higher infection rates, and the paper does not introduce any.
Levy takes on both of two central claims in the paper—one about infection rates in Manhattan relative to other boroughs and the second about high infection rates in neighborhoods adjacent to subway lines. According to Levy, "neither is even remotely correct."
The details of Levy's counterargument are best left to the source article, which is linked below, although other public health and transit experts also spoke out against the findings of Harris's paper, as evident in an article written by Aaron Gordon for Motherboard.
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