The life cycle and genomic structure of influenza A virus allow it to evolve and exchange genes easily. The virus's genetic material consists of eight separate RNA segments encased in a lipid membrane studded with proteins. To reproduce, the virus binds to and then enters a living cell, where it commandeers cellular machinery, inducing it to manufacture new viral proteins and additional copies of viral RNA. These pieces then assemble themselves into new viruses that escape the host cell, proceeding to infect other cells. No proofreading mechanism ensures that the RNA copies are accurate, so mistakes leading to new mutations are common. What is more, should two different influenza virus strains infect the same cell, their RNA segments can mix freely there, producing progeny viruses that contain a combination of genes from both the original viruses. This "reassortment" of viral genes is an important mechanism for generating diverse new strains.
Different circulating influenza A viruses are identified by referring to two signature proteins on their surfaces. One is hemagglutinin (HA), which has at least 15 known variants, or subtypes. Another is neuraminidase (NA), which has nine subtypes. Exposure to these proteins produces distinctive antibodies in a host, thus the 1918 strain was the first to be named, "H1N1," based on antibodies found in the bloodstream of pandemic survivors. Indeed, less virulent descendants of H1N1 were the predominant circulating flu strains until 1957, when an H2N2 virus emerged, causing a pandemic. Since 1968, the H3N2 subtype, which provoked the pandemic that year, has predominated.
The HA and NA protein subtypes present on a given influenza A virus are more than just identifiers; they are essential for viral reproduction and are primary targets of an infected host's immune system. The HA molecule initiates infection by binding to receptors on the surface of certain host cells. These tend to be respiratory lining cells in mammals and intestinal lining cells in birds. The NA protein enables new virus copies to escape the host cell so they can go on to infect other cells.
After a host's first exposure to an HA subtype, antibodies will block receptor binding in the future and are thus very effective at preventing reinfection with the same strain. Yet flu viruses with HA subtypes that are new to humans periodically appear, most likely through reassortment with the extensive pool of influenza viruses infecting wild birds. Normally, influenza HAs that are adapted to avian hosts bind poorly to the cellsurface receptors prevalent in the human respiratory tract, so an avian virus's HA binding affinity must be somewhat modified before the virus can replicate and spread efficiently in humans. Until recently, existing evidence suggested that a wholly avian influenza virus probably could not directly infect humans, but 18 people were infected with an avian H5N1 influenza virus in Hong Kong in 1997, and six died.
Outbreaks of an even more pathogenic version of that H5N1 strain became widespread in Asian poultry in 2003 and 2004, and more than 30 people infected with this virus have died in Vietnam and Thailand. The virulence of an influenza virus once it infects a host is determined by a complex set of factors, including how readily the virus enters different tissues, how quickly it replicates, and the violence of the host's immune response to the intruder. Thus, understanding exactly what made the 1918 pandemic influenza strain so infectious and so virulent could yield great insight into what makes any influenza strain more or less of a threat.
A Killer's Face
With the 1918 RNA we have retrieved, we have used the virus's own genes as recipes for manufacturing its component parts—essentially re-creating pieces of the killer virus itself. The first of these we were eager to examine was the hemagglutinin protein, to look for features that might explain the exceptional virulence of the 1918 strain.