UF Health epidemiologists and researchers unpack the genetics of a flu virus

Recently, University of Florida Health researchers discovered why an influenza virus was making young people admitted to UF Health Shands Hospital so sick: It contained a mutation that allowed it to infect the patients’ lower respiratory tracts.

Typically, flu settles in the upper airways of the lungs. The researchers knew the virus was settling deeper into the young patients’ lungs but had to determine whether a bacterial pneumonia infection caused the severity of the illness, or whether the viral infection’s penetration deep into the lungs was because of the flu itself. By sequencing samples of this flu’s gene, the researchers discovered that a mutation of the H1N1 flu virus allowed the infection to penetrate deep into the lower respiratory tract.

Knowing about this mutation will help researchers better develop vaccines to combat various forms of flu. The researchers’ findings were published recently online in the Centers for Disease Control and Prevention’s journal Emerging Infectious Diseases.“We’ve all had the flu and it’s miserable, but it’s usually in the upper airways. It usually doesn’t get down deep into the lungs,” said Nicole Iovine, M.D., Ph.D., an epidemiologist for UF Health Shands Hospital and assistant professor of medicine in the College of Medicine, division of infectious diseases and global medicine. “Of the patients admitted to the hospital and who had been diagnosed with influenza, more than 93 percent of them had this H1N1 virus.”

Nearly 400 patients with influenza were admitted to UF Health Shands Hospital during winter 2013 to 2014, and the vast majority of them had H1N1. Of these, 15 patients died, and all of these patients were younger than 65, according to the study. That the patients were both so young and so ill caught the researchers’ attention.

Iovine and researchers J. Glenn Morris, M.D., M.P.H., director of the Emerging Pathogens Institute at UF and John Lednicky, Ph.D., an associate professor in the UF College of Public Health and Health Professions department of environmental and global health, sequenced the genes of the virus samples they obtained from patients.

The researchers found a mutation in a viral protein called hemagglutinin. The protein binds to receptors on human cells, allowing the virus to infect the cell. Because of previous, unrelated research published by other scientists, UF Health researchers knew it was this protein mutation that allowed the infection to take hold in the lower respiratory tract.

Even more unusual, the H1N1 virus, including this mutation, targets people between ages 20 and 40. Typically, people who develop severe cases of the flu are those at the extremes of their lifespan: Those who are very young, and those who are very old.

The mystery remains as to why H1N1 — including this variant of H1N1 — hits younger people particularly hard.

Studying the genetics of the virus helps Lednicky predict whether flu vaccines will protect against particular strains.

“I am interested in how a virus changes and why virulence may change in particular viruses,” said Lednicky, who studies virology and the airborne transmission of pathogens. “By looking at the virus genes, I can make predictions about whether a vaccine will work.”

Depending on the effectiveness of the vaccine, health care providers can tailor their messages to the public. The annual flu vaccine protects against H1N1, but the number of patient cases with this strain of H1N1 is small enough that researchers haven’t been able to study the flu vaccine’s protection against it. The researchers also lack complete data about whether the patients reported in the paper were vaccinated, Morris said.

“The bottom line is that the flu is constantly changing,” Morris said. “What we do here at UF and particularly at the Emerging Pathogens Institute is to monitor the flu, from year to year to keep track of what’s happening.”

In all cases, Morris recommends people of all ages get the flu vaccine if their health status allows.

“The best protection remains getting the flu vaccine,” Morris said.