First big influenza genome study reveals flu evolution

Which flu did you get? TIGR scientists survey five New York flu seasons

On the eve of the 2005-06 flu season, scientists at The Institute for Genomic Research (TIGR) have captured influenza evolution in action. In a study published in this week’s journal Nature, the researchers report the first large-scale project to sequence the influenza virus. The study offers a unique snapshot of the rapidly evolving flu virus in a human population–and a new strategy for surveillance.

In the study, TIGR scientists and their colleagues sequenced 209 complete genomes of the human influenza A virus. The genomes represent virus samples, or isolates, taken from patients who visited county clinics across New York over the past five flu seasons, from 1999-2004. Almost all the influenza genomes represent the H3N2 strain, which predominated during these flu seasons. Comparing these genomes, the researchers tracked the changing virus as it moved across the region.

“This study demonstrates that genomics can help us better track the flu virus and develop more effective vaccines,” remarks first author Elodie Ghedin, who heads TIGR’s viral genomics lab. “This is perhaps the most detailed snapshot scientists have gotten of flu’s movement through communities.”

Across New York State, the researchers documented at least three distinct subpopulations (variants) of the H3N2 influenza virus over the five-year study period. In some of the flu seasons studied, these variants circulated simultaneously. That means New Yorkers weren’t all catching the same flu, but rather slightly different versions of the virus. Even within this relatively small geographic region, Ghedin says, the dynamic influenza virus showed striking diversity, with variants frequently swapping genetic material.

In fact, the researchers report, one such event explains why the 2003-04 flu vaccine offered less protection than usual.

Every flu season, a global network of scientists attempts to identify several predominant flu strains and factor them into the next season’s flu vaccine. Predictions are tricky, however, because influenza is constantly changing. In the 2002-03 flu season, the Nature study reports, a minor H3N2 variant reassorted, or genetically mixed, with the dominant strain. This reassortment yielded a new strain late in the season. The new strain quickly won out, becoming the dominant virus in the 2003-04 flu season. Because scientists had not factored this latecomer strain into the ’03-04 vaccine, however, the vaccine was less effective.

Genomics turns a new spotlight on influenza evolution. By deciphering the genomes of different influenza strains, researchers can pinpoint mutations that allow particular strains to become more virulent, adapt to infect new species, or evade immune response.

Moreover, TIGR’s high-throughput influenza genome sequencing pipeline offers a pivotal strategy for crafting emerging vaccines that work. “Right in the middle of flu season, we could determine which influenza strains are present in the population, which ones are dominant, and how well a given vaccine works,” Ghedin notes. She adds that all sequences described in the current study have been deposited in public databases, such as GenBank, which allows immediate access to the scientific community.

The new study represents the initial results from the Influenza Genome Sequencing Project, launched in 2004 by the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health. As part of this ongoing project, TIGR will sequence thousands of human flu isolates, as well as avian, equine, and swine flu isolates, to recognize influenza’s patterns of genetic change. To do so, TIGR has built an innovative viral genomics lab, which is ramping up to sequence 100 influenza genomes weekly.

Influenza poses a major public health problem. In an ordinary year, the flu kills up to a half million people worldwide. In the U.S., a typical flu season brings 36,000 deaths and 114,000 hospitalizations. Over the past century, three pandemics–in 1918, 1957, and 1968–caused millions of deaths. Today, scientists worry that virulent influenza strains in other species, such as the H5N1 bird flu strain found in poultry and migratory birds in Asia and Russia, will jump the species barrier into humans and trigger a new pandemic.

Although researchers first isolated the influenza virus in 1933, they still don’t fully understand how the virus evolves. Influenza is an RNA virus that contains eight separate RNA segments encoding genes for at least 11 proteins. This structure explains why the influenza virus constantly reassorts genetically. When two different influenza strains infect the same cell, their separate RNA segments can easily swap material, resulting in entirely new strains.

Type A influenzas (one of three major types, or genera) cause widespread flu among humans. Researchers classify type A influenzas according to structural variations in two surface proteins: hemagglutinin (HA) and neuraminidase (NA). Like changing coats, the influenza virus changes the shape of these HA or NA proteins when it accumulates minor mutations or reassorts more dramatically. The human immune system no longer recognizes the virus, and infection begins anew.

Steven Salzberg, senior author of the Nature paper, says the new work illustrates this chain of molecular events. “The study demonstrates that these influenza subpopulations, or variant strains, represent a pool of genetic resources that the influenza virus can draw upon,” says Salzberg, a researcher at TIGR and also director of the University of Maryland’s Center for Bioinformatics and Computational Biology. “Pockets of distinct flu strains spread locally, with flu evolving in different directions. Then, when one strain mingles with another, a new, dominant strain can emerge.”