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Swine Flu Pandemic (H1N1)
The 2009 flu pandemic was caused by a new strain of H1N1 influenza virus. A similar strain was endemic in pigs but was not readily transmissible to humans. In 1998 an apparent hybridisation of pig, bird and human strains created a transmissible strain which re-emerged as the 2009 ‘swine flu’
What is pandemic influenza and how does it happen?
A pandemic generally occurs when the rate at which a disease spreads exceeds what is expected and over a large region, often globally. In the case of influenza this typically happens every 10 – 30 years. Most other years only a small proportion of the population are infected and the symptoms comparatively mild.
The influenza virus is constantly evolving in small increments by the process of antigenic drift. This is where the surface proteins (haemagglutinin and neuraminidase) change progressively, eroding any immunity an individual may have to the strain. In the case of severe pandemics a major genetic change occurs to which the population has little immunity. This is invariably the result of antigenic shift where at least two strains of the virus exchange genetic material to form a hybrid subtype.
Influenzavirus A is capable of infecting humans, other mammals and birds, and although uncommon to be passed between species it is possible. Even if cross species infection occurs it is unlikely that the strain will transmit effectively within the population. However, if an individual were to become infected with two strains from two species it is possible that reassortment of genetic material could occur. The resultant antigenic shift could potentially provide a route for the strain to cross the species barrier, but to replicate and transmit effectively.
The 2009 ‘swine flu’ pandemic was the H1N1 strain of the influenza virus.
The development of H1N1 swine flu
The list below shows notable events in the development and occurrence of H1N1 influenza 
1918 - ‘Spanish Flu’ resulted in the death of 50 million people worldwide. The pandemic also effected pigs although it is uncertain in which direction the virus was transferred. It is likely however that the source of this particularly virulent strain was a cross species reassortment event.
1976 - A form of H1N1 swine flu was identified as the cause of an outbreak at a U.S. military base resulting in five cases including one death. In this outbreak the virus spread from pigs to humans, whilst previously H1N1 swine flu had been limited to pigs.
1998 – A strain of H1N1 swine flu emerged that was to become endemic on pig farms across North America. Analysis of the virus revealed that it was a triple reassortant of strains originating from pigs, humans and birds.
2009 – Global outbreak of H1N1 influenza originating in the state of Veracruz, Mexico. This strain appears to have novel surface proteins, particularly the haemagglutinin, resulting in generally low immunity.
Swine flu and Spanish flu
The history of the H1N1 strain of influenza in pigs indicates how the virus probably evolved from the lethal 1918 pandemic. Although it is unclear whether humans spread the virus to pigs or visa versa the strain became progressively less virulent over the following decades. At the same time swine H1N1 flu became common amongst pig populations in North America. Direct transmission from pigs to humans was rare and even when a zoonotic episode such as that in 1976 occurred the disease was unable to spread effectively amongst humans.
The significant factor in the evolution of the H1N1 swine flu was first identified in 1998 following an epidemic of the infection amongst swine populations in North America. Analysis revealed that the strain was a hybridised form resulting from the triple reassortment of swine, avian and human flu. The surface proteins were human in origin and the internal proteins, with the exception of three RNA polymerase coding genes, were from pigs. Two of these RNA polymerase genes were avian in origin and the other was human. It is these avian polymerase genes which are believed to have increased the strain’s virulence in humans and have also been implicated in the 1918 pandemic .
Six out of the eight viral gene segments  of the strain responsible for the 2009 H1N1 pandemic are the same as those from the 1998 outbreak providing strong evidence of the source.
Another significant factor in the virulence of an influenza strain are the surface proteins. In the case of the 2009 outbreak the haemagglutinin was the swine version meaning that if human antibodies were unable to recognise it the disease could be potentially very serious.
Swine flu caught the medical community off guard
In retrospect the milestones in the evolution of the 2009 H1N1 swine flu pandemic show a progression that is in line with our understanding of the nature of flu strains. As with all major flu pandemics the strain originated as the result of a major shift in the genetic makeup of the virus. In this case though, the precursor was identified in 1998 which could have provided advanced warning of the impending outbreak. It seems that by developing in pigs the virus was overlooked by the mainstream research establishment, although the threat was clearly real.
The resultant outbreak of ‘swine flu’ in 2009 was fortunately not as serious as some had predicted. However, it has highlighted the potential reservoir of infection that pig populations provide and more importantly their potential to act as a crucible where novel influenza viruses can emerge