They compared the genetic sequences of the collected deer samples to available human ones and found 3 that were nearly identical, which suggests direct spread. From the article:

Lastly, the genetic data suggested three spillovers of deer-adapted SARS-CoV-2 viruses back to humans—two in North Carolina and one in Massachusetts. For this, the researchers compared the deer SARS-CoV-2 sequences to sequences of viruses isolated from humans, available via public databases. In all three possible spillover cases, SARS-CoV-2 isolates from human cases were over 99.9 percent identical to deer-adapted viruses collected from deer in the corresponding states.