Influenza Virus Genetics, Reassortment, and Antigenic Shift
Influenza virus has 8 separate gene segments (made of RNA rather than DNA). When two (or more) different strains of influenza infect the same cell their gene segments go into a big pool and they can get get mixed up. This process is known as reassortment. Reassortment allows for the almost instantaneous creation of a brand new strain of virus, called antigenic shift. Influenza viruses are named for their two most important virulence genes: hemagglutinin (HA, H) and neuraminidase (NA, N). This is why influenza viruses are often referred to as H1N1, H3N2, etc. (Tamiflu is a NA inhibitor). If an H1N1 virus and an H3N2 virus infect the same cell, reassortment can lead to the emergence of a new H3N1 virus, or H1N2, etc. If the human population is not prepared immunologically for the new strain, an epidemic can result. Each year flu experts and the CDC have to predict which strains of influenza are expected to emerge in the coming year and those are the strains vaccine manufacturers produce vaccines for. If the experts guess wrong, the efficacy of the vaccine can be greatly compromised.
Why Southeast Asia?
In rural Southeast Asia, there are lots of ducks and other birds living in and around the rice paddies. In addition local farmers live in close proximity to their livestock, including pigs. This creates the perfect storm for the emergence of new strains of influenza: people living in close proximity to influenza-infected birds and influenza-infected pigs. Bird flu and swineflu, ring a bell? Through reassortment all these different viruses can exchange genetic material and create brand new viruses.