"It shouldn't have been able to pass from skunk to skunk," Worgess said.
Rabies has continued to crop up in skunks for eight years now, despite periodic vaccination campaigns. And so far this year, county officials have documented 14 rabid foxes in the Flagstaff area.
Now laboratory studies at the U.S. Centers for Disease Control and Prevention (CDC) in Atlanta appear to confirm that the fox and skunk rabies viruses are mutated forms of the bat strain.
"We can see degrees of relatedness and patterns in their genetic codes," said Charles Rupprecht, chief of the rabies program for the CDC.
This sort of rapid evolution is exactly what worries public health officials when it comes to all manner of viruses. Virologists haven't seen such fast adaptation to a new species in rabies before.
"That's why Flagstaff is such an interesting story worldwide," said David Bergman, the U.S. Department of Agriculture's state director for Arizona.
"We're watching evolution in action on the ground."
Could Rabies Become Contagious in Humans?
The Arizona rabies situation is risky, because the infected species live so close to people.
Flagstaff's sprawl in recent decades has created a perfect opportunity for rabies to mutate into species-hopping forms, the CDC's Rupprecht said.
New-home construction, often in wooded areas, has actually increased habitat and food sources for bats, skunks, and foxes. Skunks live under houses, for example, and as diggers, make themselves at home on golf courses. Bats, meanwhile, are adept at living in attics and under loose shingles.
As more rabies-susceptible animals congregate in the region, more infections can take place. And each infection is an opportunity for the virus to mutate into a more virulent form—literally upping the odds of a new strain developing.
"That's a pattern that we see all over the United States," Rupprecht said. Similar suburban development in the eastern U.S. in the late 1970s, he noted, led to the spread of raccoon rabies from the Canadian border to the Deep South.
The risk of such a virulent strain jumping to people "should be a major concern," said Hinh Ly, a molecular virologist at the Emory University School of Medicine in Atlanta, who is not involved in studies of the Arizona outbreak.
But no one is expecting the rabies strain to become a contagious, swine flu-like epidemic among humans.
Flu viruses, for one thing, tend to infect people fast, so "vaccination after exposure would be too late to prevent infection," said Elisabeth Lawaczeck, the Arizona Department of Health Services' public health veterinarian.
Rabies takes its time before going from incubation to infection, so post-exposure rabies vaccinations tend to be effective at stopping the virus. If untreated, though, rabies, which attacks the central nervous system, is often fatal in humans.
Rabies cases among animals are expected to increase as the spring and summer mating seasons bring potential pairs and rivals together. (Related: "Bat Rabies Threat Rises With Summer Temperatures.")
Already, Flagstaff has declared a 90-day pet quarantine—all dogs on leashes and all cats indoors—which began in April.
A wildlife vaccination plan could stem the virus's spread. Local and state officials enacted vaccination programs in northern Arizona in 2001 and 2005 but discontinued each effort after two years without rabies reports—the World Health Organization's standard for declaring an area rabies-free.
Now state vaccination funds have been reallocated, the USDA's Bergman said, and emergency funds are increasingly rare due to the recession.
Adding to the worries, Lawaczeck, the Arizona veterinary official, said she and other public heath officials were "very unsettled" when the first rabid fox reports came in from Flagstaff this year—and not just because of the evolutionary implications for rabies.
"This means a much wider spread of rabies," she said, "because [foxes] travel so much farther."
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