In blog posts and comments I’ve seen a few people arguing that the Mexico H1N1 influenza virus must have been around for a while — 10 years? 11 years? — because it doesn’t have any really close neighbours based on sequence.  I’m not sure where this is coming from, but the precision of the “11 years” seems strange.  Has anyone knowledgeable actually said this, or is it based on guesswork?

In any case, the notion that this H1N1 has been circulating for a decade has struck me as a great underestimate of influenza variation.  This virus is more or less 96% identical — depending on which segment you choose — to other ciruclating North American or Eurasian swine flu viruses.  That seemed like a really close agreement to me and seemed like the sort of thing that could happen really fast.

But I’m not a flu guy.  So I looked for some way to compare.  What I wanted was a series of influenza sequences with known dates and phylogeny — that is, preferably from a single outbreak or series of outbreaks with a more or less common cause.  I found that in this paper1 from Jian et al. looking at influenza outbreaks in Taiwan in the 2003-2006. I focused on the Influenza A, H1N1 type — and this represented a single flu season.

Looking at the 169 amino acid region they sequenced:

The average numbers of differences at antigenic and nonantigenic sites of H1 in 2005 and 2006 were 0.90 and 2.34, respectively.  … Moreover, we have observed that the overall average amino acid difference has steadily increased since February 2006. The average differences at antigenic and nonantigenic sites in 2005 were 0.39 and 0.67, respectively, while in the first 7 months of 2006 they were 0.98 and 2.93, respectively. 1

I’m having a little trouble exactly mapping the sequences they deposted in GenBank with the order they were isolated in and so on.  But the bottom line is that it looks as if in a single flu season, this human strain showed up to 5% divergence at the nucleic acid level.

That’s pretty much the same divergence as we’re seeing between separate outbreaks here — that is, between known North American swine flu viruses and the new Mexican H1N1.

In other words, I believe the divergence we’re seeing between the Mexican strain and known strains is pretty much what you’d expect to see in any influenza outbreak.


  1. Jian, J., Chen, G., Lai, C., Hsu, L., Chen, P., Kuo, S., Wu, H., & Shih, S. (2008). Genetic and Epidemiological Analysis of Influenza Virus Epidemics in Taiwan during 2003 to 2006 Journal of Clinical Microbiology, 46 (4), 1426-1434 DOI: 10.1128/JCM.01560-07[][]