To gain insight into the possible origins of the 2009 outbreak of new influenza A(H1N1), we performed two independent analyses of genetic evolution of the new influenza A(H1N1) virus. Firstly, protein homology analyses of more than 400 sequences revealed that this virus most likely evolved from recent swine viruses. Secondly, phylogenetic analyses of 5,214 protein sequences of influenza A(H1N1) viruses (avian, swine and human) circulating in North America for the last two decades (from 1989 to 2009) indicated that the new influenza A(H1N1) virus possesses a distinctive evolutionary trait (genetic distinctness). This appears to be a particular characteristic in pig-human interspecies transmission of influenza A. Thus these analyses contribute to the evidence of the role of pig populations as “mixing vessels” for influenza A(H1N1) viruses.
On 24 April, the World Health Organization (WHO) released the first alert indicating the occurrence of confirmed human cases of swine influenza A(H1N1) in North America . A few days later, the Centers for Disease Control and Prevention in the United States confirmed that these human influenza cases were caused by the same new influenza A(H1N1) virus . Soon after, it was proposed that the current flu outbreak is caused by a new influenza A(H1N1) virus generated from a triple reassortment of human, swine and avian viruses [2-8]. Other publications, including our study presented here, demonstrate that this new influenza A(H1N1) virus most likely evolved from recent swine viruses [9-11].
Methods and results
Protein homology analysis
We used more than 400 protein sequences to analyse the genetic evolution of the new influenza A(H1N1) virus. This set of protein sequences included polymerases PB2, PB1 and PA, hemagglutinin (HA), nucleocapsid (NP), neuraminidase (NA), matrix 1 (MP1), nonstructural 1 (NS1) encoded by the new influenza A(H1N1) virus as well as other homologous proteins from influenza viruses from past flu seasons. Phylogenetic tree topologies revealed that the closest homologies for the new influenza A(H1N1) virus are swine influenza viruses that have been circulating in the United States and Asia for the last decade (Figure 1, Supplementary materials: Figure 1 and Table 1).
Figure 1. Possible origins of the influenza 2009 A(H1N1) virus: a) hemagglutinin and b) neuraminidase proteins
These findings indicate that domestic pigs in North America may have a central role in the generation and maintenance of this virus. This idea is also supported by the observation that protein sequences of the new influenza A(H1N1) virus have close homology to proteins of swine influenza viruses that infected humans in the recent past (Supplementary materials: Figure 1, Figure 2 and Table 2). In fact, a common element of these swine influenza zoonotic transmissions was that humans (mostly swine farm workers) were in direct contact with infected pigs [12-15].
To further examine the possible genetic origins of the new influenza A(H1N1) virus, we compared all the available sequences of influenza A(H1N1) viruses circulating in North America for the last two decades (from 1989 to 2009). Protein sequences from avian, swine and human influenza viruses were obtained from the Influenza Virus Resource , a database that integrates information gathered from the Influenza Genome Sequencing Project of the National Institute of Allergy and Infectious Diseases (NIAID) and the GenBank of the National Center for Biotechnology Information (NCBI). A total of 5,214 protein sequences were found in this database. After removing identical sequences, a set of 1,699 influenza A proteins including PB2, PB1, PA, HA, NP, NA, MP1, and NS1 proteins were used for analyses of the genetic evolution of influenza A(H1N1) viruses. These analyses provide additional evidence of the role of pig populations as “mixing vessels” for influenza A(H1N1) viruses (Figure 2).
Figure 2. Genetic distinctness of the influenza 2009 A(H1N1) virus: a) hemagglutinin (HA) and b) neuraminidase (NA) proteins; c) phylogenetic trees for PB2, PB1, PA, NP, MP1, and NS1 proteins
Secondly, our analyses also revealed that the new influenza A(H1N1) virus possesses a distinctive evolutionary trait (genetic distinctness), that seems to be characteristic in pig-human interspecies transmission of influenza A (reported cases occurred in Iowa, Maryland and Wisconsin, United States between 1991 and 2006) (Figure 2, Supplementary materials: Figure 2 and Table 3).
Discussion and conclusion
Although limited in sample size, our analyses substantiate the value of molecular screening and phylogenetic assessment for understanding the evolution of influenza viruses and, most importantly, for the early detection of emerging novel viruses that could lead to influenza pandemics. Notably, our analyses revealed that the new influenza A(H1N1) virus is genetically distinct from other influenza A(H1N1) viruses that have been circulating for the last twenty flu seasons (Figure 2 and Supplementary materials: Figure 2). Influenza viruses with novel antigens (genetic drift) can escape from immune responses induced by prior infection or vaccination and can lead to a pandemic .
These observations also reiterate the potential risk of pig populations as the source of the next influenza virus pandemic. Although the role of swine as “mixing vessels” for influenza A(H1N1) viruses was established more than a decade ago [18,19], it appears that the policy makers and scientific community have underestimated it. In fact, in 1998 influenza experts proposed the establishment of surveillance in swine populations as a major part of an integrated early warning system to detect pandemic threats for humans [18,19] but, to some extent, this task was overlooked. For example, a search of influenza sequences in the Influenza Virus Resource  revealed that the total number of swine influenza A sequences (as of 19 May 2009) is ten-times smaller than the corresponding number of human and avian influenza A sequences (4,648 compared to 46,911 and 41,142 sequences, respectively). More significantly, in some countries, such as the United States, the national strategy for pandemic influenza  assigned the entire preparedness budget (3.8 billion US dollars) for the prevention and control of avian A(H5N1) influenza, overlooking the swine threat [20-22]. In our (the authors’) opinion, in this plan, a substantial effort was dedicated to prevent and contain the foreign threat of Asian avian flu, neglecting the influenza threat that the North American swine population presents . Specifically, we believe that the aforementioned strategy ignores the swine farm and industry workers which constitute the population at higher risk of contracting and spreading the hypothetical pandemic influenza virus [24-26].
The current new influenza A(H1N1) outbreak caused by a virus of swine origin represents a new challenge for animal and human health experts. Our institution, the College of Veterinary Medicine at the National Autonomous University of Mexico (Universidad Nacional Autonoma de Mexico, UNAM) is placing a strong emphasis on the establishment of influenza surveillance in swine and avian species to identify novel genetic assortment of the new influenza A(H1N1) and other influenza viruses circulating in Mexico. For example, since 2002, we have been monitoring the genetic evolution of influenza A viruses circulating in Mexican poultry farms . Now, a similar surveillance system will be applied to swine farms. This effort prioritises the use of genetic distinctness as a marker for the detection of novel viruses that could lead to influenza pandemics.
The recent influenza pandemic threat in North America reveals that it is time to take action towards the development of a systemic surveillance system which integrates phylogenetic information of influenza viruses circulating in humans and livestock.
Supplementary materials: Figure 1, Figure 2, Table 1, Table 2, Table 3:
- World Health Organization (WHO). Influenza-like illness in the United States and Mexico. Epidemic and Pandemic Alert and Response (EPR). 24 April 2009. Available from: http://www.who.int/csr/don/2009_04_24/en/index.html
- Centers for Disease Control and Prevention (CDC). Update: swine influenza A(H1N1) infections – California and Texas, April 2009. MMWR Morb Mortal Wkly Rep 2009;58(16):435-7.
- Cohen J, Enserink M. Infectious diseases. As swine flu circles globe, scientists grapple with basic questions. Science. 2009;324(5927):572-3.
- Centers for Disease Control and Prevention (CDC). Swine influenza A(H1N1) infection in two children – Southern California, March-April 2009. MMWR Morb Mortal Wkly Rep 2009;58(15):400-2.
- Anonymous. Swine influenza: how much of a global threat? Lancet. 2009;373(9674):1495.
- Cohen J. Swine flu outbreak. Out of Mexico? Scientists ponder swine flu's origins. Science. 2009;324(5928):700-2.
- Butler D. Swine flu goes global. Nature. 2009;458(7242):1082-3.
- Cohen J. Swine flu outbreak. Flu researchers train sights on novel tricks of novel H1N1. Science. 2009;324(5929):870-1.
- Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, Balish A, et al. Antigenic and Genetic Characteristics of Swine-Origin 2009 A(H1N1) Influenza Viruses Circulating in Humans. Science. 22 May 2009 [Epub ahead of print] DOI: 10.1126/science.1176225
- Solovyov A, Palacios G, Briese T, Lipkin WI, Rabadan R. Cluster analysis of the origins of the new influenza A(H1N1) virus. Euro Surveill. 2009;14(21):pii=19224. Available from: http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=19224
- Novel Swine-Origin Influenza A (H1N1) Virus Investigation Team. Emergence of a Novel Swine-Origin Influenza A (H1N1) Virus in Humans. N Engl J Med. 22 May 2009. [Epub ahead of print].
- Gray GC, McCarthy T, Capuano AW, Setterquist SF, Olsen CW, Alavanja MC. Swine workers and swine influenza virus infections. Emerg Infect Dis. 2007;13(12):1871-8.
- Wentworth DE, Thompson BL, Xu X, Regnery HL, Cooley AJ, McGregor MW, et al. An influenza A (H1N1) virus, closely related to swine influenza virus, responsible for a fatal case of human influenza. J Virol. 1994;68(4):2051-8.
- Gregory V, Lim W, Cameron K, Bennett M, Marozin S, Klimov A, et al. Infection of a child in Hong Kong by an influenza A H3N2 virus closely related to viruses circulating in European pigs. J Gen Virol. 2001;82(Pt 6):1397-406.
- Olsen CW, Karasin AI, Carman S, Li Y, Bastien N, Ojkic D, et al. Triple reassortant H3N2 influenza A viruses, Canada, 2005. Emerg Infect Dis. 2006;12(7):1132-5.
- Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L, Tatusova T, et al. The influenza virus resource at the National Center for Biotechnology Information. J Virol. 2008;82(2):596-601.
- Hilleman MR. Realities and enigmas of human viral influenza: pathogenesis, epidemiology and control. Vaccine 2002;20(25-26):3068-87.
- Webster RG. Influenza: an emerging disease. Emerg Infect Dis. 1998;4(3):436-41.
- Ito T, Couceiro JN, Kelm S, Baum LG, Krauss S, Castrucci MR, et al. Molecular basis for the generation in pigs of influenza A viruses with pandemic potential. J Virol. 1998 Sep;72(9):7367-73.
- Homeland Security Council. National Strategy for Pandemic Influenza. President of the United States: Washington; November 2005. Available from: http://www.pandemicflu.gov/plan/federal/pandemic-influenza.pdf
- Comments from the Center for Biosecurity of UPMC on the National Strategy for Pandemic Influenza: Implementation Plan. Biosecur Bioterror. 2006;4(3):320-4.
- Mair M. National strategy for pandemic influenza released; $3.8 billion appropriated for pandemic preparedness. Biosecur Bioterror 2006;4(1):2-5.
- Staff of the Center for Biosecurity of UPMC. National strategy for Pandemic Influenza and the HHS Pandemic Influenza Plan: thoughts and comments. Biosecur Bioterror 2005;3(4):292-4.
- Gray GC, Kayali G. Facing pandemic influenza threats: the importance of including poultry and swine workers in preparedness plans. Poult Sci 2009;88(4):880-4.
- Ramirez A, Capuano AW, Wellman DA, Lesher KA, Setterquist SF, Gray GC. Preventing zoonotic influenza virus infection. Emerg Infect Dis. 2006;12(6):996-1000.
- Myers KP, Olsen CW, Setterquist SF, Capuano AW, Donham KJ, Thacker EL, et al. Are swine workers in the United States at increased risk of infection with zoonotic influenza virus? Clin Infect Dis. 2006;42(1):14-20.
- Escorcia M, Vázquez L, Méndez ST, Rodríguez-Ropón A, Lucio E, Nava GM. Avian influenza: genetic evolution under vaccination pressure. Virol J. 2008;5:15.