So

your position is that the term itself is racist now, but wasn't racist then?

If that was the case, do you think that perhaps the New York Times would want to have updated their article with a note that they apologize for the usage of the racist terminology? Are you upset that they haven't? Is that offensive?

Would referring to a company formed in China, but with operations around the world, as Chinese be racist also?

It might not be desirable to emphasize this particular aspect of the virus, or it might evidence one's own particular animus toward China, but the idea that the term "Chinese virus" is racist is just evidence that "racist" is being used as a catch-all for "something that may have negative impacts on non-white people, even if those negative impacts are directly caused by other people."