Herbert Van Kruiningen stood before the open door of the avian post-mortem laboratory in the Department of Pathobiology, wearing a mask, surgical gloves, and a knee-length plastic apron over the white coat of an animal doctor, ready to resume a gruesome job.

Behind him, spread on a long stainless steel table sloped towards a drain for easy cleansing, lay 39 dead crows being prepared for a necropsy - like a human autopsy - by two other members of the department's faculty, which includes 14 veterinary pathologists. A stench wafted out.

"This is one of society's first lines of defense in an epidemic-type situation," said Van Kruiningen, referring to the deadly mosquito-borne virus that caused an outbreak of encephalitis last month and is suspected of having caused the death of hundreds of birds in southern Connecticut, as well as the death of five New York residents. "We're examining as many birds as possible to see whether they have come into contact with the virus."

For the last three weeks, Van Kruiningen, a professor of pathobiology, and two of his colleagues - assistant professor Richard French, a veterinary pathologist, and associate professor Antonio Garmendia, a virologist - have been at the center of tracking the spread of the elusive disease, said to be like the West Nile-like encephalitis virus found in Africa. The study is being conducted under the auspices of UConn's Northeastern Research Center for Wildlife Diseases, which is directed by Van Kruiningen.

The symptoms of viral encephalitis include fever, headache, neurological disorders and even death. Birds have been dying by the hundreds in Connecticut, a situation that mirrors what's been happening in New York and New Jersey, and state health officials suspect many of the birds may have been killed by the virus.

Since mid-September, increasing numbers of dead birds have been brought to the pathobiology laboratory for analysis by local public health, animal control and state Department of Environmental Protection officials. The lab is the headquarters of the state's Veterinary Diagnostic Laboratory, which is geared to responding to newly developing disease problems.

In the lab, Van Kruiningen and his team have meticulously weighed and recorded details about each bird sent for analysis. During the necropsy, each bird's brain is removed, with half of the tissue sent to the Connecticut Agricultural Experiment Station in New Haven for virus testing. The other brain halves are processed at UConn for microscopic analysis.

Van Kruiningen, French and Garmendia paused last week from their lab work to face a bevy of television cameras and some unanswerable questions. What's killing the birds? When will it end? Are you alarmed?

Van Kruiningen didn't like that word, alarmed. "We're certainly concerned about it," he replied.

"There are a lot of unknowns," he added. "This is an exotic virus that was not supposed to be in this part of the world."

The purpose behind testing the dead birds, he said, is to know the scope of the epidemic and to use the location where dead birds are found to help detect infection in new areas.

Nearly 200 bird carcasses, mostly from towns in Fairfield County but extending east to Orange, Milford and Wallingford in New Haven County and Wethersfield in Hartford County, have been brought to the lab.

While the majority have been crows, there were also red-tailed hawks, woodpeckers, starlings, finches, robins, pigeons, and one wild turkey, said Van Kruiningen. "Sadly we're starting to see a greater variety. And we won't know about song birds that live in meadows and forests. If they are dying, no one will find them."

So far, out of more than 200 autopsies performed by the UConn pathologists, seven crows have tested positive for the West Nile-like encephalitis virus. All were found in Fairfield County. Van Kruiningen suspects that as more results come in, many other birds will also test positive.

Because of the way tissue samples are processed, there is at least a four-day delay between when the pathobiologists remove tissue for analysis and when they can actually conduct microscopic examinations.

The process includes first preserving the tissue in formalin - a diluted formaldehyde that kills any microbes in the sample. Next the tissue goes though a series of baths in alcoholic solvents that remove fat and water. Finally the tissue is thinly sliced and mounted on glass slides for microscopic study.

The microscopic analysis "is a second way of developing evidence for a viral infection," explained French. "This virus appears to have a predilection for the brain, which is why we are only preparing samples from brain tissue."

Displaying a glass slide of crow brain tissue on a television monitor, French pointed out inflammatory cells surrounding blood vessels. "These are the hallmarks of viral encephalitis," he explained.

The appearance of a new virus in an environment where few animals have any resistance is a classic recipe for an epidemic, noted Garmendia, who has been taking blood samples from all the birds undergoing necropsy in the UConn lab.

"We have to determine whether there are any antibodies against the virus," he noted. "In my opinion, there is probably a much larger population of birds being exposed to this new virus. Some of them will not die, but will make antibodies and survive."

Birds that survive may remain carriers of the virus, he added. Birds carry the disease and mosquitoes transmit the infection to humans. Garmendia said he does not anticipate a large public health problem this year, because the drop in temperatures that comes with the fall will cause a large decline in the mosquito population.

He does believe, however, that the virus could survive the winter and reappear when mosquitos re-emerge next spring. "The big question is whether this virus will remain in this country," Garmendia noted. "If it becomes established, we will have to be on the look out for it every year."

David Bauman