Tuesday, April 28, 2009

Applying phylogenetics: Did the California H1N1 swine flu come from Ohio?

Just as we (in Biol 105) finish up studying how phylogenetic trees are estimated, and how they might be used to answer interesting questions, comes this highly topical example - microbiologist and science blogger Sandra Porter spent a happy afternoon applying phylogenetic analyses to try and answer the health scare du jour:

This afternoon, I was working on educational activities and suddenly realized that the H1N1 strain that caused the California outbreak might be the same strain that caused an outbreak in 2007 at an Ohio country fair. Here's the data.

Once I realized that the genome sequences from the H1N1 swine flu were in the NCBI's virus genome resources database, I had to take a look.

And, like eating potato chips, making phylogenetic trees is a little bit addictive. Or maybe it was just the adrenaline rush that hit when I realized that every tree was telling me the same thing.

What did those trees say?

Read the full blog post to study the results yourself, and see what you think of the remarkable concordance between the trees, providing a plausible answer to the question of where this virus may have originated.

In the process, Dr. Porter has also given us all a glimpse at the working product of a fresh analysis - raw results hot off the computer before they are published in a peer-reviewed journal! Is this a first for the blogosphere? I don't know, but given the high level of public interest, I can see why one might want to get the results out quickly. Surely some top science journal would be interested in publishing this quickly as well?

Thanks to Porter's blog, we all get to see how genomic data available in the public domain can be used to help address problems that might affect us in real time! How cool is that?! As I try to impress upon my students every time we discuss the subject: Phylogenies are not just static graphic depictions of inferred relationships between organisms long gone - trees of dead wood, so to speak: they also serve as working models of ongoing evolutionary processes! And often enough, they help us pinpoint the origins of new diseases, in turn helping us develop treatment strategies before the outbreak gets too far out of hand. And how is that for putting those phylogenetic trees to work?

Meanwhile, Tara Smith, of Aetiology (also on ScienceBlogs) following up on Porter's big discovery, notes that the peer-reviewed paper describing the Ohio swine flu strain came out only recently. And here's the bit that really raises the eyebrow, if not the hair on your head:

I also assume this is where the human-avian-swine reassortant claim came from. The authors note that:

The H1N1 viruses contain the HA and NA from the classical swine virus and the internal genes from the triple reassortant H3N2 viruses (rH1N1); the H1N2 viruses contain the HA from the classical swine virus and the NA and internal genes from the triple reassortant H3N2 viruses (Karasin et al., 2002; Webby et al., 2004). Contemporary triple reassortant viruses were demonstrated to have acquired a PB1 gene of human virus origin; PA and PB2 genes of avian virus origin; and the remaining internal genes, M, NS, and NP, of swine virus origin, thus giving rise to the triple reassortant designation (Zhou et al., 1999).

So what it looks like to me is that this isn't a *new* reassortant virus, but is closely related to one that had already been identified in swine--and that had already caused an outbreak in humans right here in the US.

So why is the virus getting so much more media attention this time around? Is the strain in Mexico really the same or different? And if it is the same (or close) how did it get from Ohio to Mexico City and back to Texas and California? Gotta love that globalization, eh!



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