SAN FRANCISCO Thousands of blacktailed and mule deer are dropping dead from an exotic virus attacking fawns and adults in more than a dozen counties in Northern California.

The devastating disease is still a mystery to the wildlife veterinarians who a

re working around the clock to learn ab

out it.

From Yreka to the foothills of Sonora and wild places in Marin and Sacramento counties, the deer deaths have touched off a new uncertainty about how profoundly the virus will affect the already stressed population.

''We suspect they will gain immunity and in subsequent years be less susceptible. But we don't know how serious it will be next year,'' said Dr. Pamela Swift, wildlife veterinarian at the state's Wildlife Investigations Laboratory at Rancho Cordova

.

Starting in the hot days of summer, newborn fawns began foaming at the mouth. They could hardly breathe. Hundreds started dying. Others pulled through the respiratory illness, but other hot spots of die-offs emerged hundreds of miles away.

The viral disease in deer has been confirmed in Nevada, Siskiyou, Lake, Tuolumne and Sacramento. Other reports are on record from El Dorado, Amador, Placer, Yuba, Sutter, Mariposa and Santa Clara. None has been reported in Southern California.

To date, more than 2,000 Columbia blacktailed and mule deer have died out of the statewide population of 700,000, according to the California Department of Fish and Game, which runs the Rancho Cordova lab.

The first accounts of deer deaths from rural residents in June and July at first made scientists suspect that the outbreaks were associated with some kind of human pollution. Top suspects were golf course runoff or herbicides.

By August, scientists at the University of California-Davis Veterinary Diagnostic Laboratory had identified the killer as a group of viruses called adenoviruses. The viruses, which can transform DNA, are passed from deer to deer through direct contact and bodily secretions.

''The viral diseases are hitting animals that for ot

her purposes are very healthy,'' said Dr. Leslie Woods, a veterinarian at the UC lab who is working on the cases.

''The reason we're attributing the death to adenoviruses is we see damage to the blood vessels. It's the best smoking gun that we've got.''

Scientists now are working to isolate the virus in a culture from the tissue itself.

''Once you isolate it in culture, then you can do all the fancy things like finding out which species of adenovirus it is closest to,'' Woods said.

Woods does know that

the virus seems specific to a species. Humans need not fear catching it. ''An adenovirus in turkey usually won't affect pigs.''

Other viruses have also attacked deer, including blue tongue, the disease that killed about 300 at Clear Lake, Calif., in 1989 and 1990.

David Jessup, a Fish and Game veterinarian, said blue tongue has been around since the 1940s, unlike the new and exotic adenoviruses. It's not bad this year because the strain around doesn't happen to be very ''hot,'' or pathogenic, he said.

Why the adenovirus viruses struck in 1993 is a mystery, and some scientists speculate that the rains released them into the environment.

Once the adenovirus in the deer is isolated, Fish and Game can learn more about it, Swift said.

Scientists could then develop a serological test, which would tell them if a deer h

ad been exposed. They could tell when the virus appeared in a herd and how it spread among counties.

That way, Fish and Game can study live deer and not be

forced to conduct tests on carcasses.

''I don't want to

go out and start killing deer that are sick,'' Swift said. ''I want them to get well.''

Meanwhile, veterinarian Swift is quick to warn that people should stay away from a sick deer.

''Leave it alone. Don't feed the deer,'' Swift said. ''Feeding causes them to congregate and more readily transmit (the disease) from deer to deer.''

If the deer is dead, her wildlife lab would like to collect the body for investigation.

Recently, two does and a large buck died after confused wanderings at Rancho Murietta, a private community near Sacramento.

''First we thought it was poisoning. To have three down at one time was a little odd for us. But Fish and Game told us about the new virus, and we put warnings not to feed the deer in our local paper,'' said James Noller, chief of security.