Influenza A Virus in Swine – Moving beyond 2009

13 April 2012, at 12:00am

Facing the swine and human health issues with influenza proactively with science, transparency, and cooperation is both a challenge and an opportunity, according to A.L. Vincent of the USDA and co-authors in the US and Brazil as they addressed the <em>International Symposium on Emerging and Re-Emerging Diseases in Pigs</em> in 2011.

Surveillance for influenza A viruses (IAV) circulating in pigs and other non-human mammals has been chronically under-funded and virtually non-existent in many areas of the world (1). This deficit is in spite of our knowledge that influenza is a disease shared between man and pig from at least as far back as the 1918 Spanish Flu Pandemic.

In March-April 2009, a novel pandemic H1N1 emerged in the human population in North America (2) and demonstrated in a public forum the paucity of data on influenza viruses in swine. The gene constellation of the emerging virus was demonstrated to be a combination of genes from swine influenza A viruses (SIV) of North American and Eurasian lineages that had never before been identified in swine or other species. The emergent H1N1 quickly spread in the human population and the outbreak reached pandemic level 6 as declared by the World Health Organization on 11 June 2009.

Although the eight-gene segments of the novel virus are similar to available sequences of corresponding genes from SIV from North America and Eurasia, no closely related ancestral IAV with this gene combination has been identified in North America or elsewhere in the world (3,4).

Other than sporadic transmission to humans (5,6), swine influenza A viruses of the H1N1 subtype historically have been distinct from avian and other mammalian H1N1 influenza viruses in characteristics of host specificity, serologic cross-reactivity, and/or nucleotide sequence. The emergence of the 2009 pandemic H1N1 (pH1N1) virus brought a heightened awareness to the evolution and epidemiology of influenza A viruses in swine and presents a new era of challenges and opportunities for understanding and controlling influenza in pigs.

North American Triple Reassortant Swine Viruses

Swine influenza was first recognised in pigs in the Midwestern US in 1918 as a respiratory disease that coincided with the human pandemic known as the Spanish flu. Since then, it has become an important disease to the swine industry throughout the world. The first influenza virus was isolated in 1930 by Shope (7) and was demonstrated to cause respiratory disease in swine that was similar to human influenza. The classical swine lineage H1N1 (cH1N1) derived from the 1918 pandemic was relatively stable at the genetic and antigenic levels in US swine.

The epidemiology of IAV in pigs dramatically changed after 1998 when triple reassortant viruses containing gene segments from the classical swine virus (NP, M, NS), human virus (PB1, HA, NA), and avian virus (PB2, PA) (8) became successfully established in the pig population (9). The human lineage PB1, avian lineage PB2 and PA and swine lineage NP, M, and NS found in contemporary swine influenza viruses are referred to as the triple reassortant internal gene (TRIG) constellation (10) and the vast majority of the characterised swine viruses from the US and Canada contain the TRIG, regardless of subtype.

After their emergence, the H3N2 viruses reassorted with cH1N1 swine IAV (11,12). Reassortant H1 viruses are endemic with the H3N2 viruses in most major swine producing regions of the U.S. and Canada. Since 2005, H1N1 and H1N2 viruses with the HA gene derived from human viruses emerged and spread across the US in swine herds (13). The HAs from the human-like swine H1 viruses are genetically and antigenically distinct from classical swine lineage H1s. However, their TRIG genes are similar to those found in the TRIG cassette of the contemporary swine triple reassortant viruses.

To represent the evolution of the currently circulating North American H1 viruses, a cluster classification has been proposed. Viruses from the classical H1N1 lineage-HA evolved to form ?-, ß-, and ?-clusters based on the genetic make-up of the HA gene; whereas H1 subtypes strains with HA genes most similar to human seasonal H1 viruses form the ?-cluster (13).

All four HA gene cluster types can be found with neuraminidase genes of either the N1 or N2 subtype. The HA from the ?-cluster viruses were shown to have most likely emerged from two separate introductions of human seasonal HA from H1N2 and H1N1 viruses and are differentiated phylogenetically by two distinct sub-clusters, ?1 and ?2, respectively (14). HAs of the ?-cluster were paired either with an N1 or N2 gene of human virus lineage and not of swine N1 lineage. The H1 SIV are evolving by drift and shift while maintaining the TRIG backbone and the resulting viruses differ genetically and antigenically with obvious consequences for vaccine and diagnostic test development (14).

Eurasian Viruses

Swine IAV with genetic lineages that are distinct from the North American TRIG viruses evolved in Europe and Asia (reviewed in (15)). Although cH1N1 swine viruses previously circulated in Europe, Asia and many other parts of the world, they were eventually replaced by a new lineage in Europe, a wholly avian H1N1 that emerged in 1979. The avian-lineage H1N1 was subsequently identified in Asia in 1993.

Human-lineage H3N2 distinct from those in North America also emerged in Europe and Asia in the 1970s. Additionally, a human-like H1N2 emerged in pigs in Great Britain in the 1990s. A recent European surveillance study reported the continued circulation of avian-like H1N1, human-like H3N2 and human-like H1N2 in swine. All three subtypes were detected in Belgium, Italy and Spain, while only H1N1 and H1N2 viruses were found in UK and Northwestern France (16). The epidemiology of influenza viruses in Asia is complicated by the presence of North American and European lineage viruses, subsequent reassortant swine viruses between the two lineages, and reports of unique avian-lineage viruses. A complete description of IAV in Asian swine is beyond the scope of this paper.

Pandemic H1N1

The pH1N1 possesses a unique genome with six gene segments (PB2, PB1, PA, HA, NP and NS) with the closest known genetic lineage being the triple-reassortant influenza viruses of the North American swine lineage and the M and NA genes derived from a Eurasian lineage of swine influenza viruses (17).

The 2009 pandemic influenza became infamously known as ‘swine flu’ due to the phylogenetic origin of the gene segments. However, the unique combination of gene segments had never before been recognised in swine and since the recognition of the pandemic, the epidemiology in humans has not been affected by the subsequent human to pig transmission and outbreaks in pigs (17). The initial documented swine outbreaks were preceded by reported human influenza-like illness during the pandemic (18). The 2009 pH1N1 was shown to replicate efficiently in the lower and upper respiratory tract of experimentally infected pigs and to cause a clinical disease comparable to that typically observed during common enzootic influenza virus infection in swine (19-21).

Early reference to the 2009 pH1N1 as ‘swine flu’ led to unnecessary alarm over the safety of pork meat products and culminated in the ban of exported pork from the US by several countries, resulting in billions of dollars in lost revenue for the US swine industry. However, contamination of fresh pork meat with the novel virus was experimentally excluded (22).

Immediately after the onset in humans, cases of infection of pigs with the p2009 H1N1 were reported in different areas of the world. The first case was detected on 28 April 2009 in Canada in a farm with pigs that were not previously vaccinated against swine influenza (18, 23). Based on observations thus far, it is likely that the virus will continue to jump from humans to susceptible pigs with subsequent pig-to-pig transmission and establishment of yet another endemic virus in swine populations around the world. The 2009 pH1N1, a virus shared between people and pigs, has the potential to further change the epidemiology of influenza viruses in human and swine populations.

None of the eight genes of the 2009 pH1N1 cluster tightly with the genes of SIV circulating in the US prior to the outbreak in humans (3). In the phylogenetic analyses of each gene segment, the 2009 pH1N1 formed a distinct and independent branch from the US swine lineage genes in viruses collected prior to 2009 and continues to do so. This suggests that neither the 2009 pH1N1 nor closely related progenitor viral genes were present in US swine influenza viruses prior to 2009. A closely related progenitor virus with the same eight-gene constellation has yet to be identified in swine or other species, although a 2004 swine virus with 7/8 of the 2009 pH1N1 genome was identified in Hong Kong, China (3). The temporal gap between the closest known ancestor virus and the emergence of the pandemic virus in 2009 underscores the need for improved surveillance in animal hosts worldwide, as well as human hosts in under-represented parts of the world.

A recent study demonstrated an enhancement of disease and pathologic changes in the lungs of pigs vaccinated with a virus with the H1 HA derived from human seasonal influenza virus (?-cluster SIV) and challenged with 2009 pH1N1 (24). These data suggest that non-neutralising inactivated vaccine-induced immune response contributed to the enhanced disease. This phenomenon has the potential to be realised in the swine population due to the concurrent circulation of genetically diverse H1 SIV among swine vaccinated with inactivated virus vaccines that are potentially mismatched to the circulating strains.

The vaccine associated enhanced respiratory disease (VAERD) underscores the need for improved surveillance, antigenic mapping and vaccine strain selection. Additionally, this phenomenon may have relevance in the human population with some vaccine formulations as suggested by the association between the 2008-09 seasonal human vaccine and pH1N1 illness during 2009 (25) and low avidity, complement fixing antibodies in the lungs of fatal cases of pH1N1 in humans (26). Additional studies are in progress to further evaluate the kinetics and mechanism of VAERD in pigs.

Relevance to Human Health

The trivalent human vaccine no longer contains the seasonal H1N1 that circulated in the human population from the mid-1970s until 2009 due to its recent replacement by the pH1N1. If this remains the case in the coming years, the youngest subset of the human population may not have immunity against viruses related to the swine ?-cluster. The pig population may now serve as a reservoir of influenza genes historically shown to be successful in humans, such as the ?-cluster HA and NA; the pH1N1 HA, NA, and M; as well as the TRIG genes of human and pH1N1 virus lineage. This, combined with sporadic infections with avian-lineage viruses in pigs, may provide the right opportunity for continued IAV reassortment and emergence in pigs.

The potential for further zoonotic transmission events of novel viruses from pigs to people remains an unknown but possible risk that must be considered.


Surveillance and genetic characterisation of influenza viruses associated with respiratory disease outbreaks in pigs are necessary for monitoring the evolution of viruses in the pig population to aid minimally in the development of sensitive and specific diagnostic tests. In addition, antigenic characterisation is critical to fully understand the relevance of genetic changes for vaccine strain selection, and vaccine efficacy must be evaluated minimally by serologic activity when new variants arise.

The 2009 pH1N1 underscores the potential risk to human and animal populations of influenza virus subtypes and genotypes that may evolve with the SIV TRIG backbone and/or other virus lineages. Increased surveillance for the pH1N1 as well as reassortants between pH1N1 and endemic SIV in the swine and human populations is essential to understand the dynamic ecology of influenza A viruses in susceptible host populations.

The World Organisation for Animal Health (OIE) and the Food and Agriculture Organization of the United Nations (FAO) formed OFFLU in 2005, a network of laboratories formally organised to demonstrate expertise in the animal health sector for surveillance, diagnostics, research, and control of highly pathogenic avian influenza H5N1.

Influenza viruses circulating in swine and other animal hosts have recently been added to the OFFLU objectives and the potential for collaboration and exchange of information and resources between all influenza sectors is supported by OFFLU, with WHO also a contributing member.

Although pigs may support the emergence of new viral reassortants, they may more often be the victim of cross-species transmission from people or birds than they are the source of new viruses. However, this cross-species transmission and the true directionality of virus movement cannot be fully understood without surveillance.

A global surveillance system in pigs has not yet come to fruition, despite the existence of several successful local and regional programmes. A limitation of the regional approach is that the information is not always integrated and shared across species and regions, diminishing the effectiveness of surveillance efforts. Furthermore, unless a wide variety of pigs and geographical locations are sampled, the information may be biased and lead to inaccurate interpretation and/or decisions.

The necessary global integration and sharing of data and resources for SIV will be addressed through the OFFLU network but will require grass roots support from veterinarians and the swine industry. Facing the swine and human health issues with influenza proactively with science, transparency, and cooperation is our challenge and opportunity now and in the coming years.


1. Anon. 2009. Animal farm: pig in the middle. Nature, 459(7249):889.
2. Garten, R.J. et al. 2009. Science, 325(5937):197-201.
3. Smith, G.J.D. et al. 2009. Nature, 459:1122-1125.
4. Trifonov, V., H. Khiabanian and R. Rabadan. 2009. New England Journal of Medicine, 361(2):115-119.
5. Myers, K.P., C.W. Olsen and G.C. Gray. 2007. Clin Infect Dis, 44(8):1084-1088.
6. Shinde, V. et al. 2009. New England Journal of Medicine, 360(25):2616-2625.
7. Shope, R.E. 1931. J Exp Med, 54:373-385.
8. Zhou, N.N. et al. 1999. J Virol, 73(10):8851-8856.
9. Webby, R.J. et al. 2000. J Virol, 74(18):8243-8251.
10. Vincent, A.L. et al. 2008. Adv Virus Res, 72:127-154.
11. Webby, R.J. et al. 2004. Virus Res, 103(1-2):67-73.
12. Karasin, A.I. et al. 2002. J Clin Microbiol, 40(3):1073-1079.
13. Vincent, A.L. et al. 2009. Virus Genes, 39:176-185.
14. Lorusso, A., et al. 2010. J Gen Virol.
15. Brown, I.H. 2000. Vet Microbiol, 74(1-2):29-46.
16. Kyriakis, C.S. et al. 2011. Zoonoses Public Health, 58(2):93-101.
17. Dawood, F.S. et al. 2009. N Engl J Med, 360(25):2605-2615.
18. Howden, K.J. et al. 2009. Can Vet J, 50(11):1153-1161.
19. Vincent, A.L. et al. 2010. Influenza and Other Respiratory Viruses, 4(2):53-60.
20. Brookes, S.M. et al. 2009. Vet Rec, 164(24):760-761.
21. Lange, E. et al. 2009. J Gen Virol, 90(Pt 9): 2119-2123.
22. Vincent, A.L. et al. 2009. PLoS ONE, 4(12):e8367.
23. Weingartl, H.M. et al. 2010. J Virol, 84(5):2245-2256.
24. Gauger, P.C. et al. 2011. Vaccine, 29(15): 2712-2719.
25. Skowronski, D.M. et al. 2010. PLoS Med, 7(4):e1000258.
26. Monsalvo, A.C. et al., 2010. Nat Med.


Vincent A.L., A. Lorusso, K.M. Lager, P.C. Gauger, M.R. Gramer and J.R. Ciacci-Zanella. 2011. Influenza A Virus in Swine – Moving beyond 2009. Proceedings of the 6th International Symposium on Emerging and Re-Emerging Pig Diseases. Barecelona, Spain, June 2011.

Further Reading

- You can view the Proceedings of the 6th International Symposium on Emerging and Re-Emerging Pig Diseases by clicking here.

Further Reading

- Find out more information on influenza in pigs by clicking here.

April 2012