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The cause of the 2009 swine flu was an influenza A virus type designated as H1N1. In 2011, a new swine flu virus was detected. The new strain was named influenza A (H3N2)v. Only a few people (mainly children) were first infected, but officials from the U.S. Centers for Disease Control and Prevention (CDC) reported increased numbers of people infected in the 2012-2013 flu season. Currently, there are not large numbers of people infected with H3N2v. Unfortunately, another virus termed H3N2 (note no "v" in its name) has been detected and caused flu, but this strain is different from H3N2v. In general, all of the influenza A viruses have a structure similar to the H1N1 virus; each type has a somewhat different H and/or N structure.

Many researchers now consider that two main series of events can lead to swine flu (and also avian or bird flu) becoming a major cause for influenza illness in humans.

First, the influenza viruses (types A, B, C) are enveloped RNA viruses with a segmented genome; this means the viral RNA genetic code is not a single strand of RNA but exists as eight different RNA segments in the influenza viruses. A human (or bird) influenza virus can infect a pig respiratory cell at the same time as a swine influenza virus; some of the replicating RNA strands from the human virus can get mistakenly enclosed inside the enveloped swine influenza virus. For example, one cell could contain eight swine flu and eight human flu RNA segments. The total number of RNA types in one cell would be 16; four swine and four human flu RNA segments could be incorporated into one particle, making a viable eight RNA-segmented flu virus from the 16 available segment types. Various combinations of RNA segments can result in a new subtype of virus (this process is known as antigenic shift) that may have the ability to preferentially infect humans but still show characteristics unique to the swine influenza virus (see Figure 1). It is even possible to include RNA strands from birds, swine, and human influenza viruses into one virus if a single cell becomes infected with all three types of influenza (for example, two bird flu, three swine flu, and three human flu RNA segments to produce a viable eight-segment new type of flu viral genome). Formation of a new viral type is considered to be antigenic shift; small changes within an individual RNA segment in flu viruses are termed antigenic drift (see figure 1) and result in minor changes in the virus. However, these small genetic changes can accumulate over time to produce enough minor changes that cumulatively alter the virus' makeup over time (usually years).

Second, pigs can play a unique role as an intermediary host to new flu types because pig respiratory cells can be infected directly with bird, human, and other mammalian flu viruses. Consequently, pig respiratory cells are able to be infected with many types of flu and can function as a "mixing pot" for flu RNA segments (see figure 1). Bird flu viruses, which usually infect the gastrointestinal cells of many bird species, are shed in bird feces. Pigs can pick these viruses up from the environment, and this seems to be the major way that bird flu virus RNA segments enter the mammalian flu virus population. Figure 1 shows this process in H1N1, but the figure represents the genetic process for all flu viruses, including human, swine, and avian strains.