Researchers have literally unearthed clues as to why the 1918 influenza pandemic was so deadly. Using fragments of the flu genome from Army autopsy tissues and a body buried in the freezing Alaskan permafrost, researchers have assembled genes from the 1918 flu virus. SSRL’s x-ray beams then revealed the structural secrets of a protein encoded by one of the genes.

A ‘ribbon’ representation created from data taken at SSRL shows part of the hemagglutinin (HA) protein from the 1918 influenza virus. The receptor binding site is where the flu protein attaches to human lung cells. The two patches—one found only in bird forms of the protein—may have contributed to increased infection rates during the 1918 pandemic. (Image courtesy of James Stevens and Ian Wilson, The Scripps Research Institute)

"It’s been known for many years that the 1918 pandemic was one of the greatest killers ever seen," said Ian Wilson (Scripps Research Institute). Between 20 and 40 million people died worldwide, including an abnormally high proportion of healthy young adults, who rarely die from influenza.

At the time, people did not know influenza was caused by a virus. To find surviving samples of genetic material, Jeffery Taubenberger (Armed Forces Institute of Pathology) and colleagues searched through the Army’s large set of preserved autopsy tissues and took biopsies from Alaskans buried in the permafrost. "Whole villages were wiped out by the flu," Wilson said.

From those samples, Taubenberger figured out the sequence of the flu’s genetic information. The virus has eight gene segments that give instructions for making at least 11 proteins. Wilson and James Stevens (Scripps Research Institute) produced one of the viral proteins, called hemagglutinin (HA), and used SSRL’s protein crystallography beam line to see the coils, stalks and heads that make up HA’s structure. Their results appeared in the journal Science.

The intricate shape helps explain why the 1918 flu virus was unusually virulent. HA is the most abundant protein on the virus’s surface, making it the main target for the immune system to recognize and attack. HA binds to human lung cells and enables the virus to get into the cell inside sacs called vesicles. HA then undergoes a change in shape and helps the viral and vesicle membranes to fuse, allowing the infection to gain ground.

The structural analysis shows that the 1918 HA protein is more closely related to avian (bird) forms than previously believed. Flus that infect birds and pigs also have eight gene segments, corresponding to human flu, but the proteins look somewhat different.

"That’s one of the reasons influenza is so successful," Wilson said. "It can re-sort these segments from different sources, say one from a bird and the rest from a human." The mixture is devastating because our immune system has no protective antibodies to avian or swine proteins that it has never seen before being infected. In the three flu pandemics last century, Wilson said the HA gene and a second viral gene were replaced by segments from pigs or aquatic birds. "For the 1918 flu, we were interested to see if it’s more avian-like or has features of both, to see why it was so virulent," he said.

Two features in HA’s shape particularly stand out as potentially contributing to the extraordinarily high infection and mortality rates observed in 1918. The receptor binding site (for the virus to attach to human cells) is narrow, and is only a single mutation away from a known swine-avian virus. The mutation makes the binding site slightly larger, which could increase affinity for human cells.

The researchers also observed two patches rich in histidine (an amino acid) which may boost the ability of HA to fuse to the vesicle membrane in order to escape and replicate itself inside human cells. One of the patches is found only in avian forms of HA. "[This] provid[es] tantalizing evidence of a direct jump of this virus from birds to the human naïve population," Wilson added.

"There are 11 gene products involved, and they probably all play a role," he said. "This is just a start as far as we’re concerned."