We could see, for example, that the part of the 1918 HA that binds with a host cell is nearly identical to the binding site of a wholly avian influenza HA. In two of the 1918 isolates, this receptor-binding site differs from an avian form by only one amino acid building block. In the other three isolates, a second amino acid is also altered. These seemingly subtle mutations may represent the minimal change necessary to allow an avian-type HA to bind to mammalian-type receptors.
But while gaining a new binding affinity is a critical step that allows a virus to infect a new type of host, it does not necessarily explain why the 1918 strain was so lethal. We turned to the gene sequences themselves, looking for features that could be directly related to virulence, including two known mutations in other flu viruses. One involves the HA gene: to become active in a cell, the HA protein must be cleaved into two pieces by a gut-specific protein-cutting enzyme, or protease, supplied by the host. Some avian H5 and H7 subtype viruses acquire a gene mutation that adds one or more basic amino acids to the cleavage site, allowing HA to be activated by ubiquitous proteases. In chickens and other birds, infection by such a virus causes disease in multiple organs and even the central nervous system, with a very high mortality rate. This mutation has been observed in the H5N1 viruses currently circulating in Asia. We did not, however, find it in the 1918 virus.
The other mutation with a significant effect on virulence has been seen in the NA gene of two influenza virus strains that infect mice. Again, mutations at a single amino acid appear to allow the virus to replicate in many different body tissues, and these flu strains are typically lethal in laboratory mice. But we did not see this mutation in the NA of the 1918 virus either. Because analysis of the 1918 virus's genes was not revealing any characteristics that would explain its extreme virulence, we initiated a collaborative effort with several other institutions to re-create parts of the 1918 virus itself so we could observe their effects in living tissues.
A new technique called plasmid-based reverse genetics allows us to copy 1918 viral genes and then combine them with the genes of an existing influenza strain, producing a hybrid virus. Thus, we can take an influenza strain adapted to mice, for example, and give it different combinations of 1918 viral genes. Then, by infecting a live animal or a human tissue culture with this engineered virus, we can see which components of the pandemic strain might have been key to its pathogenicity.
For instance, the 1918 virus's distinctive ability to produce rapid and extensive damage to both upper and lower respiratory tissues suggests that it replicated to high numbers and spread quickly from cell to cell. The viral protein NS1 is known to prevent production of type I interferon (IFN)—an "early warning" system that cells use to initiate an immune response against a viral infection. When we tested recombinant viruses in a tissue culture of human lung cells, we found that a virus with the 1918 NS1 gene was indeed more effective at blocking the host's type I IFN system.
To date, we have produced recombinant influenza viruses containing between one and five of the 1918 genes. Interestingly, we found that any of the recombinant viruses possessing both the 1918 HA and NA genes were lethal in mice, causing severe lung damage similar to that seen in some of the pandemic fatalities. When we analyzed these lung tissues, we found signatures of gene activation involved in common inflammatory responses. But we also found higher than normal activation of genes associated with the immune system's offensive soldiers, T cells and macrophages, as well as genes related to tissue injury, oxidative damage, and apoptosis, or cell suicide.