It's of particular concern for endangered species and can threaten the conservation mission of zoos, the scientists wrote in the journal Current Biology.
Brain infection encephalitis struck two polar bears at the Zoological Gardens in Wuppertal, Germany, killing a 20-year-old female, the BBC reported Friday.
A 16-year-old recovered after suffering symptoms for several weeks, zoo officials said.
Gene sequencing of DNA and RNA from the dead bear suggested the culprit was a strain of herpes virus normally found in zebras.
"These viruses do not seem to respect species boundaries and in fact, we don't really know whether they have any," Klaus Osterrieder from the Free University Berlin said.
Zoos present a particular problem as animals from different continents and habitats that would never live alongside each other in the wild are brought in close proximity with each other.
"The visitors to the zoo want to see as many different animals from different places as possible, which is good but there has to be control," Alex Greenwood of the Leibniz-Institute for Zoo and Wildlife Research said.
"Knowledge is the best weapon."