Can a genetic model predict next year’s flu strain? A physicist says yes

By Geoffrey Mohan Los Angeles Times Published Feb 28, 2014 at 12:01AM

LOS ANGELES — The seasonal flu has met its enemy, and it’s calculus.

A theoretical physicist and computational biologist analyzed the genetic code of thousands of strains of Influenza A that occurred over a 44-year period to create a model that accurately predicts which strain will prevail in the pitched evolutionary battle between human antibodies and the rapidly mutating virus.

Their method proved more accurate for selecting an appropriate vaccine than the current method used by public health officials, according to a report published online Wednesday in the journal Nature.

The researchers, from the University of Cologne in Germany and Columbia University, examined Influenza A/H3N2, a seasonal strain that causes thousands of deaths annually. They focused on the H part — short for hemagglutinin, a spike-shaped protein that seeks out sugars in human cells and binds to them, allowing the virus to inject its deadly code.

Human antibodies — naturally launched or gigged into action by vaccines — engage in a constant arms race with this wildly mutating protein, making flu vaccination season something of an educated guessing game. World health officials have been reasonably accurate in identifying which resistant strains are emerging as a new threat. But their method has a lot of uncertainty. A study in 2010, in fact, called several popular diagnostic methods “questionable.”

Inaccuracy also is at the heart of the survival for a virus, which shuffles its code enough to create variations that don’t show up on the radar of the human immune system.

“This is a really fast-evolving virus,” said study co-author Marta Luksza, a computational biologist at Columbia University. “Individual strains are very short-lived. Very, very rarely are there two identical strains. They mutate, they infect another individual. But they do share common mutations still.”

Luksza and co-author Michael Laessig estimated the frequency of these mutations in the viral RNA and factored in such variables as infection rates to come up with a model predicting a strain’s evolutionary fitness.

Since the researchers already knew the outcome of the evolutionary arms race from the record of flu strains from 1968 to 2012, they tested whether their model would have identified the fittest strains. It predicted the rise of the correct lineage in 93 percent of cases.