“At this point, what we can say is that we haven’t found the cryptic lineages in human databases, and we have looked all over,” said Monica Trujillo, a microbiologist at Queensborough Community College and an author of the new paper.

The researchers themselves are torn about the lineages’ origins. Some lean toward the explanation that the virus is coming from people whose infections aren’t being captured by sequencing. But others suspect that the lineages may be coming from virus-infected animals, possibly the city’s enormous population of rats. Even then, the favored theory can change from day-to-day or hour-to-hour.

Answers remain elusive.

“I think it’s really important that we find the source, and we have not been able to pin that down,” said John Dennehy, a virologist at Queens College and an author of the paper.