In the May 26 (2011) issue of Nature, Vijaykrishna et al. address patterns of evolution and transmission exhibited by swine influenza A viruses (SwIV) isolated from pigs beings slaughtered in Hong Kong between May 1998 and January 2010.  Although the focus of the study is on viruses that circulate in swine, this study is relevant to human medicine and public health because these viruses can serve as the ancestors of viruses that infect people. In southern China, all of the major lineages of SwIV co-circulate with both avian and human influenza A viruses. Some influenza A viruses of human and avian origin can infect swine, thereby creating the opportunity for recombination between them and SwIV.  The authors identify three main lineages of SwIV circulating in swine: classical swine viruses (CS), Eurasian avian-like viruses (EA), and triple reassortants that contain genes from respectively, swine, avian, and human viruses (TRIG).  The available data suggest that the CS lineage was dominant in swine prior to 1998.  Since about 2000, viruses of the EA, and later, TRIG lineages have been isolated from swine, and now the EA lineage (H1N1) is dominant (as assessed by the relative frequency of isolates corresponding to each lineage).

The authors suggest that the movements of substantial numbers of live pigs from outlying Chinese provinces to Hong Kong may be facilitating the diversification of SwIV through reassortment of genes from different lineages.  Vijaykrishna et al. note that the changes over time in SwIV genomes are less rapid, periodic, and predictable than is the case for human influenza viruses, which are notable for annual strain replacements.  Perhaps the pattern of human influenza A virus dynamics is determined by the behavior of the human influenza A virus population as a single gene pool.  In contrast, according to the authors, the SwIV population does not yet behave as as a single gene pool. 

The authors believe that future increases in global movements of SwIV could greatly influence virus evolution and transmission and this possibility deserves monitoring.  However, current knowledge and understanding of the processes involved will not permit certain predictions of the impact on genomic and antigenic diversification of viral transmission over long distances.

A key observation of this study is that the EA-reassortant viruses exhibit continuing antigenic evolution after initial generation and may undergo more rapid antigenic drift of the surface proteins than non-reassortant viruses.  In addition, influenza-naïve pigs infected with EA viruses appear to shed more virus than influenza-naïve pigs infected with CS or TRIG viruses. Together, the more rapid rate of antigen change and the greater likelihood of transmission for some EA viruses, in comparison to viruses from the other major lineages, may account for the recent dominance of EA lineages over CS and TRIG lineages.

This study clearly indicates the relevance of both evolutionary and ecological factors to patterns of viral evolution.  Furthermore, phylogenetic analysis, along with high-resolution genomic characterization and antigenic assessment, played an absolutely crucial role in elucidating the patterns of influenza A virus evolution in swine.  Improved understanding and better prediction of the dynamics of genomic and antigenic change for influenza A viruses of both swine and humans will likely affect decisions relating to vaccine design and distribution and thereby influence public health and medical practice.   

References

Vijaykrishna D, Smith GJ, Pybus OG, Zhu H, Bhatt S, Poon LL, Riley S, Bahl J, Ma SK, Cheung CL, Perera RA, Chen H, Shortridge KF, Webby RJ, Webster RG, Guan Y, Peiris JS. Long-term evolution and transmission dynamics of swine influenza A virus. Nature 2011 May 26;473(7348):519-22. PubMed PMID: 21614079.