Flu in pigs has been known for 90 years, and on the surface, it may appear as though little has changed. We still suspect flu when a high percentage of pigs have a sudden onset of barking cough, especially during temperature fluctuations in the fall or spring. However, the influenza viruses responsible for current flu outbreaks are quite different from past versions, and they represent a variable and dynamic population of viruses with increasing genetic diversity. This diversity confounds the ability to stimulate protective immunity through vaccine use and, perhaps, even through natural infection.
Prior to 1998, only one flu virus (now referred to as the classical H1N1 influenza virus) was responsible for seasonal outbreaks of swine flu. This flu was described as the sudden onset of coughing and respiratory distress that dissipated almost as quickly as it started. For roughly 80 years after the human pandemic influenza virus jumped to pigs around 1918, the H1N1 virus remained relatively stable in swine, and serologic studies suggested only sporadic and transient introductions of viruses of another subtype or from another species.
click image to zoom In 1998, a severe influenza-like disease surfaced almost simultaneously in pigs in North Carolina, Iowa, Minnesota and Texas. Causing these outbreaks was a new subtype introduced into swine from the human population; it was identified as influenza A viruses of the H3N2 subtype. Unlike the classical H1N1 virus, the H3N2 subtype was a triple reassortant. This means that it contained a mixture of gene segments derived from influenza viruses from swine, human and avian species. The triple-reassortant virus quickly became endemic in U.S. swine due to a lack of immunity in the pig population as well as the H3N2 virus’ successful adaptation to the swine host. By the end of 1999, the H3N2 virus was detected throughout the Midwest, and once established, it didn’t take long before other variant influenza viruses began to emerge due to viral reassortment between the H3N2 and classical H1N1 viruses. Although the H3N2 virus is currently endemic in North American swine, its introduction had a significant impact on the current and future variation of influenza viruses in pigs. There are now three subtypes of swine influenza viruses (H1N1, H3N2 and H1N2) that circulate in the swine population.
Influenza viruses have a unique genetic stucture that consists of eight different gene segments. This is unlike other swine viruses, such as porcine reproductive and respiratory syndrome virus, porcine circovirus or pseudorabies virus, which have linear non-segmented genomes. When two different subtypes of influenza virus infect the same pig (such as simultaneous infection with H1N1 and H3N2), gene segments can interchange between viruses through a process called viral reassortment. The influenza viruses that emerge after reassortment can pick up a different gene(s) and represent a new variant virus in the swine population that may not be completely cross-protected by immunity against the two original viruses. (See Figure 1.)