Minor variants of flu strains, which are not typically targeted in vaccines, carry a bigger viral punch than previously realized, according to a new study that examined samples from the 2009 pandemic in Hong Kong.
The findings show that minor strains can be transmitted along with major ones and can replicate and elude immunizations.
“A flu virus infection is not a homogeneous mix of viruses, but, rather, a mix of strains that gets transmitted as a swarm in the population,” says Elodie Ghedin, professor in New York University’s biology department and College of Global Public Health.
“Current vaccines target the dominant strains, because they are the ones that seem to infect the largest number of individuals. But our findings reveal an ability of minor strains to elude these vaccines and spread the virus in ways not previously known.”
It’s long been known that the Influenza A virus is marked by a high level of genetic diversity. However, scientists’ knowledge largely stems from the dominant strain, that is targeted by vaccines. Less understood is the diversity of minor strains and how they’re able to spread.
For the study, published in the journal Nature Genetics, scientists wanted to figure out how many viral particles are transmitted when afflicted with the flu and how many could replicate when they transmit.
To examine this phenomenon, researchers performed whole genome deep sequencing of upper nasal cavity swabs taken from confirmed 2009 Hong Kong flu cases and from their household contacts.
Using sophisticated sequencing methods, the team could not only identify variants in flu strains, but also quantify what was being transmitted between infected individuals.
The results showed that, as expected, most carried the dominant virus—H1N1 or H3N2. But, they also all carried minor strains and variants of the major and minor strains. What was surprising was how readily these variants were transmitted across the studied individuals.
“The combination of unique data, sequencing approaches, and mathematical methods create a nuanced picture of the transmission of diversity during a pandemic,” says study coauthor Benjamin Greenbaum, assistant professor at the Tisch Cancer Institute at the Icahn School of Medicine at Mount Sinai.
“We were able to look at the variants and could link individuals based on these variants,” Ghedin says. “What stood out was also how these mixes of major and minor strains were being transmitted across the population during the 2009 pandemic—to the point where minor strains became dominant.”
Researchers from the University of Pittsburgh, the University of Hong Kong, and the University of Sydney are coauthors of the study.