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United States Department of Agriculture

Agricultural Research Service

Research Project: H1N1 INFLUENZA A VIRUS IN SWINE SUPPLEMENTAL RESEARCH PROGRAM Title: The changing face of swine influenza virus

item Vincent, Amy
item Gauger, Phillip -

Submitted to: Trade Journal Publication
Publication Type: Trade Journal
Publication Acceptance Date: October 30, 2011
Publication Date: November 7, 2011
Citation: Vincent, A.L., Gauger, P.C. 2011. The changing face of swine influenza virus. Pork Magazine. Available:

Technical Abstract: "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 than in the past and represent a variable and dynamic population of influenza viruses with increasing genetic diversity. This diversity confounds the ability to stimulate protective immunity through the use of vaccines and occasionally, 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 was 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 only sporadic and transient introductions of influenza viruses of another subtype or from another species were suggested by serologic studies. In 1998 a severe influenza-like disease was observed almost simultaneously in pigs in North Carolina, Iowa, Minnesota and Texas. The cause of these outbreaks was a new subtype introduced into swine from the human population and were 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 to this specific subtype in the general 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 virus. 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. Indeed, there are now three subtypes of swine influenza viruses (H1N1, H3N2 and H1N2) that circulate in the North American swine population. Influenza viruses have a unique genetic structure that consists of eight different gene segments. This is unlike other swine viruses, such PRRSV, PCV2, or pseudorabies virus, which have a single genome. 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 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. Influenza viral reassortment and the emergence of variant viruses in swine will certainly continue and the resulting genetic and antigenic diversity may have multiple consequences for swine producers. Like humans, some species of birds, and other mammals, swine can be infected with human and avian adapted influenza viruses, which has designated pigs as "mixing vessels" for influenza viruses from different species. This physiology of the swine respiratory tract along with the number of swine-adapted viruses endemic in swine populations around the world may potentially increase the risk of viral reassortment between human, avian and swine influenza viruses. The human 2009 pandemic H1N1 influenza virus was a triple reassortant that became infamously known as "swine flu" due to the suggested origin of the virus in swine. The pandemic H1N1 virus is now endemic in swine worldwide due to human movement and subsequent transmission to pigs. This is one major reason flu vaccination of farm personnel working with swine is important – to prevent human to swine transmission. Swine producers should also be aware that current influenza vaccines used in swine may not protect against new variant viruses that emerge due to viral reassortment or through the gradual change or antigenic drift of a resident virus. Although commercial inactivated vaccines contain multiple strains representing viruses currently circulating in swine, it is difficult for biological companies to change their vaccines as often as the virus changes in the swine population or to cover all of the existing antigenic variants possible in the US. This has encouraged the use of autogenous vaccines made from viruses specific to a particular farm and under the recommendation of the herd veterinarian. However, autogenous vaccines are subject to the same potential lack of cross-protection that can occur when a herd is exposed to a new or multiple viruses. Thus, mismatching between the vaccine strain and the strain currently infecting a group of pigs may remain a common occurrence. It is unknown why it took over 80 years before new subtypes emerged and were consistently detected in swine in the US. These viruses may have been present but remained undetected due to more primitive methods of detection and genetic analysis at that time. However, there were sporadic reports of reassortant viruses in pigs before 1998 that were unable to sustain sufficient pig to pig transmission to become endemic. Viruses currently circulating in U.S swine have all been triple reassortant viruses with a similar set of swine, human and avian lineage gene segments. It is possible this particular combination of genes permitted influenza viruses to maintain a level of transmission or reassortment to become successful in the swine population and combined with modern production practices, a "perfect storm" developed by chance. Ultimately we can only speculate as to why the diversity of influenza viruses has increased over the last 13 years. Genetically and antigenically diverse influenza viruses will continue to emerge in the future and have an impact on modern swine production and possibly human health as well. The potential emergence of a pandemic virus in swine with the ability to infect humans should remain a serious concern for the swine industry. However, industry consequences due to influenza virus detections in both the human and swine populations can be avoided through monitoring and surveillance of emerging viruses in all susceptible species around the world, swine included. This requires engaging both human and animal health officials, researchers and diagnostic laboratories in a cooperative effort that will benefit all involved. Access to this information would prove particularly valuable to veterinarians and swine producers through the development of efficacious influenza vaccines. The knowledge we gain has the ultimate goals of protecting the swine population from costly flu-related respiratory disease, protecting our industry from misinformation, and protecting the human population our industry feeds.

Last Modified: 8/25/2016
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