Software predicts dangerous variants of influenza viruses

December 01, 2009

Text: Tim Schröder

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Evolution of the H3N2 flu virus: Phylogenetic tree for the gene sequence of the surface protein hemagglutinin. The color... [more]

Evolution of the H3N2 flu virus: Phylogenetic tree for the gene sequence of the surface protein hemagglutinin. The color of the end nodes indicates the time at which a particular variant was isolated. This enables scientists to trace the emergence of the different virus strains and predict possible new variants. [less]

Evolution of the H3N2 flu virus: Phylogenetic tree for the gene sequence of the surface protein hemagglutinin. The color of the end nodes indicates the time at which a particular variant was isolated. This enables scientists to trace the emergence of the different virus strains and predict possible new variants.

© MPI for Informatics

© MPI for Informatics

During the cold winter months, a sneeze on an airplane or a cough on a train is enough to make us all think of the flu. And since spring 2009, a new pathogen has been traveling the world, accompanying people by air and sea from America to all other continents. It even made newspaper headlines in fall 2009: the new H1N1 virus.

By mid-January 2010, 22,000 people around the world had died of the infection commonly referred to as the “swine flu”. Just how many people have been infected is anyone’s guess. What is certain, however, is that H1N1 has presented humanity with the first case of global influenza, the first pandemic of the 21st century. And yet, up to now, the virus has proven relatively harmless: in 1918, a predecessor of the new H1N1 virus was responsible for the deaths of almost 50 million people. That pandemic went down in history as the Spanish flu. Strangely, this strain of the virus mainly claims the lives of strong young people, while the old and weak tend to remain unharmed.

Flu vaccine development – a race against the clock

For a long time, doctors had no explanation to offer for this. It was not until a few years ago that researchers were able to observe a similar phenomenon in monkeys. The pathogen clearly allows the immune system to “boil over.” If a person is infected, his or her immune response releases an excess of infection messengers – inflammation-promoting substances that are supposed to help fight the pathogen, but that attack the body’s own tissues in the process. The immune systems of strong young people, in particular, simply produce too much of a good thing here.

Scientists are now very familiar with the flu virus. It has long been classified into different groups that can be clearly differentiated on the basis of genetic characteristics and typical protein structures. Large volumes of vaccine are produced against human flu viruses every year, with the intention of protecting against infection. However, sometimes the viruses mutate so rapidly and unexpectedly in some corner of the world that humans are unable to act against them in time. A new pathogen that is not targeted by existing vaccines spreads quickly. The fight against flu viruses is thus, above all, a race against the clock.

Will the scientists succeed in tracking down a new virus variant in time before it establishes itself globally in the next impending flu epidemic? Only then can manufacturers adapt the vaccines to the new pathogens before they trigger a major flu epidemic. The researchers usually win this race. Around every four years, however, the viruses outrace them.

The scientists from the Max Planck Institute for Informatics are thus arming themselves with computing power in the war against the flu virus. The experts working with Alice Carolyn McHardy are developing software that specializes in extracting secrets from the genetic material of viruses and bacteria. One aim of the bioinformaticians is that computers will one day be able to detect, in viral genomes, suspicious patterns that betray the presence of the next trigger of a global flu epidemic – even before the flu season has begun.