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Chico State

On the Hunt for Avian Influenza Virus

Liz Bianchini performs lab work
Tyler Wright / Student Photographer

Biological Sciences Teaching Associate Liz Bianchini working at a lab on Wednesday, July 12, 2017, in Chico, Calif. (Tyler Wright/Student Photographer)


Elizabeth Bianchini and Jessica Burris take swabs from ducks laid on a table
Chico State students Elizabeth Bianchini, left, and Jessica Burris take cloacal swabs from freshly killed waterfowl at Upper Butte Basin Wildlife Area. The swabs will be taken back to the University lab to extract and test RNA for influenza viruses. (Jessica Bartlett / University Photographer)

Graduate student Liz Bianchini admits the sampling side of her research is less than glamorous.

The master’s candidate for biology burrows into her jacket in the frigid morning air as she waits for hunters and their day’s bounty at Upper Butte Basin Wildlife Area in hopes they’ll spare a few minutes for science. If they say yes, she gets down to the dirty work, taking a quick cloacal swab of the freshly killed waterfowl and dropping the cotton tips into vials.

“It’s so different than working in a lab. It’s definitely not for everybody,” Bianchini said, noting the cold, mosquitoes, dead birds, duck butts, and blood. “I wouldn’t trade it for anything right now.”

Her work is part of a multiyear research project led by Chico State virologist Troy Cline to identify and characterize viruses in migrating waterfowl. By studying avian influenza strains in ducks and other birds along the Greater Northern Pacific Flyway, they hope to inform public health measures, wildlife management, and safeguards to the US poultry industry while limiting the threat of human exposure to devastating viruses.

Cline initiated the project in 2014, one year after arriving at the University. Chico, he thought, was a prime spot for such research because of its position on the major migratory path—with 60 percent of all waterfowl in the Pacific Flyway visiting the Central Valley.

Elizabeth Bianchini hands off a sample to Troy Cline.
Elizabeth Bianchini hands off a sample to Chico State virologist Troy Cline, who is leading the multiyear study into avian influenza viruses. (Jessica Bartlett / University Photographer)

“This is ground zero for where to go to find interesting influenza viruses that could be coming into North America,” he said.

By January’s end, he and his team of students had collected more than 2,065 samples over their four-year project. For the last four years, they have spent most fall and winter Saturdays at the designated wildlife area 45 minutes south of Chico. With cooperation from hunters and the California Department of Fish and Wildlife, which manages the reserve, they collect their specimens and bring them back to Holt Hall for testing and analysis.

The lab work is an extensive process of extracting and testing RNA for influenza virus to establish flu genome sequencing. Every specimen is recorded into a database, along with details about the waterfowl it originated from, including species, gender, and age. Those records then can be compared with those being logged around the globe.

Liz Bianchini examines samples in the Holt Hall lab.
Once Bianchini has her cloacal swabs from the field, she returns to the Holt Hall lab to extract and test RNA for influenza virus to establish flu genome sequencing. (Tyler Wright / Student Photographer)

“I like the immediate applicability to the value of the work that we are doing,” Cline said. “These viruses are being monitored across the US and the world. By having this snapshot, we can help tell how these viruses are moving and interacting with waterfowl hosts.”

Waterfowl naturally carry influenza viruses in their intestines without ever showing signs of the disease or suffering the consequences. While the duck viruses that the Cline lab finds are not likely to be contagious to humans, influenza viruses are good at shape-shifting. They can acquire the ability, through random mutation or genetic re-assortment, to infect other species, such as humans or domestic poultry. If and when they begin to infect people, they can spread quickly and severely among the human population because of a lack of immunity.

Closeup of duck wing feathers
Biology professor Jay Bogiatto fans out the wings of a duck as part of his identification process to determine species, age, and sex, which will be logged along with the sample. (Jessica Bartlett / University Photographer)

For Bianchini, assisting on this project is a dream come true.

“I still remember getting my first microscope at 10 . . . My entire Facebook feed is science news,” she said. “I have been reading articles about viruses since I was in junior high.”

She admits she has a fierce fascination with subtyping viruses and that her true passion lies in pathogenic viruses—the kind that can cause mass mayhem, like the 1918 Flu Pandemic.

She revels in knowing the work of Cline’s team provides groundwork for medical research in combating viruses ranging from seasonal flu strains to pandemics.

“You never know what we might find. We could call the CDC and say, ‘Guess what we found?’” she said. “It’s a motivator to stay here and work on my master’s. I really like knowing the work I do helps the public.”

When Cline initiated the project in 2014, the world was beginning to see the emergence of H5N8 in the United States for the first time. This virus quickly combined with viruses already circulating in the United States to form a novel H5N2 virus that resulted in a widespread outbreak in 2015 and the loss of millions of chickens and turkeys. While it’s still not associated with human influenza and scientists believe it would cause only mild disease in people, the devastation it previously caused and the potential for it to mutate into something more devastating remains a cause for concern.

That first year, Cline’s team detected two highly pathogenic H5 strains—including the initial detection of the H5N8 virus—in Butte County. They’ve also found three H7N3 viruses, and the H7 strain has caused human infections in other parts of the world before. By completing flu genome sequencing on those and other samples, they have added to the greater narrative about how certain viruses arrive in North America and how they have evolved.

“That helps us put pieces of the puzzle together,” Cline said.

Like hunting or birdwatching, the team’s swab collection can be an unpredictable endeavor. With the occasional, “pop, pop, pop,” of gunfire sounding across the reserve, camouflage-clad hunters periodically pull up in dusty pickups and climb out, hunting dogs watching excitedly as they walk over with a string of birds.

“Look at the species coming in,” gushed biology professor Jay Bogiatto, an ornithology specialist who has volunteered his time to add key details to the project’s data set.

A longtime hunter and birder, Bogiatto’s been happy to spend his Saturdays on this work, helping the researchers add identification characteristics to every specimen log. Students crowd around him as he fantails the waterfowl’s feathers and explains how the coloring and condition indicate species, sex, and age.

He can’t help but marvel at the variety. A single day’s collection might include greater white-fronted geese, American widgeon, cinnamon teals, snow geese, northern shovelers, mallards, Northern pintails, and gadwalls.

Bogiatto too, is happy to spare his time for science if it means protecting those populations for generations to come while also looking out for the humans who enjoy them.

“It’s a really worthwhile project,” he said. “And I never get tired of looking at waterfowl and happy hunters.”