For years, virologists have been searching for the mechanism that allows mild bird flu viruses to turn into dangerous variants. Virologists at Erasmus MC have now uncovered the missing step: during replication, the virus’ copying machine (the polymerase) can get stuck and accidentally adds an extra fragment, making the virus more harmful.
Bird flu viruses pose a constant threat to both animals and humans, but the so-called highly pathogenic variants are particularly dangerous. They cause massive mortality in poultry. Unlike the low-pathogenic, milder variants, they do not remain confined to the lungs and intestines of the animals but spread through the bloodstream to many organs, leading to severe disease in many animal species, and sometimes in people.
Cracking a 40-year-old puzzle
That low-pathogenic viruses can transform into highly pathogenic viruses has been known for more than 40 years. But how this happens remained a mystery—until now. “It’s the holy grail of flu virology,” says molecular virologist Mathilde Richard from the Department of Viroscience at Erasmus MC. “Many scientists search for the answer, but no one could crack the code. We only got on the right track in the last five years of our 15-year quest. Our findings have been published today in Science.”
A “printer jam” in the virus
The researchers discovered that certain pieces of RNA sequences—a molecule like DNA that carries genetic information—often cause errors during virus replication. Flu viruses copy their genetic material using enzymes called polymerases. They are like printers: they use RNA as template to “print” a new RNA strand.
“During the copying of the genetic material, the RNA template can loop back on itself, tightening the polymerase like a knot in a tie. This “strangling” effect jams the polymerase, much like a printer that gets stuck and inserts new characters in a line. These accidental additions can make the virus more dangerous and deadly. And because many RNA viruses have polymerases that work in similar ways, we think that the same type of copying error could occur in other viruses.”These copying errors were detected in both bird and mammalian cells. “The change happens within the virus itself and is not dependent on the host,” Richard explains.
Steps leading to the discovery
This breakthrough was made possible due to recent advances on the structure of the polymerase, using new tools that allow researchers to freeze enzymes in action and then analyse them in minute detail under a special microscope (cryogenic electron microscopy). “These discoveries changed our understanding of how flu viruses replicate their genomes and helped us to devise the hypothesis central to this work”, says Richard. In the present work, Richard and colleagues also used cryogenic electronic microscopy and directly imaged the polymerase trapped by the RNA template (image, panel D), providing the final piece of evidence to prove the model.
What now?
“Now that the mechanisms underlying the emergence of highly pathogenic viruses have been unravelled, we can also learn to predict which viruses may become highly pathogenic and which will not”, says Richard. This will help to quickly identify variants that may become more dangerous and target these with eradication programs.
Tribute to Mathis Funk
Most of this research was carried out by researcher Mathis Funk. After completing his studies at prestigious French Grandes Écoles and university, Mathis joined Richard’s team in 2019 and soon became a pillar of the group. “When he obtained the last set of results finally proving the hypothesis, he burst into my office out of breath and was ‘over the moon’”, Richard recalls. Sadly, Funk passed away before he could share his findings with the world. Richard and her team did so on his behalf, out of respect and as a tribute to their beloved colleague.
‘We are incredibly proud of him and of his work. His passion for science, exceptional talent in bioinformatics, and groundbreaking research on bird flu viruses have left a deep and lasting impact on our field. His curiosity, creativity, and dedication were an inspiration to all who knew him, whether up close or from afar. This work was his passion; it is now his legacy. The article is dedicated to his memory.’
