Tuesday, April 28, 2009 - 15:01
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.
UPDATE: I'm not so certain anymore that the strains are the same. I'm doing some work with nucleic acid sequences to look further at similarity.
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?
They all said the California swine virus is most closely related to a swine flu virus from Ohio and very different from other H1N1 viruses that have infected humans. In fact, in some cases, it seems like the H1N1 virus is very similar to a virus that caused an outbreak in 2007 at an Ohio country fair (1).
Okay, let's look at the data. I used H1N1 (and a couple of H1N2) protein sequences from Swine and Humans between Jan 1 2006 and today. This gave between 324 and 600 sequences for each tree and every case, the California sequences clustered with those from the Ohio pigs.
And now, the data.
1. PB1
2. PB2
3. NA
4. PA
5. NP
6. M1
7. M2
8. HA
For every single protein sequence tested, the 4 California isolates clustered with the sequence from the country fair pig from Ohio.
In a few cases, one other Ohio pig isolate (2) was part of the cluster. The sum of the phylogenetic analyses are compelling and support the hypothesis that the California H1N1 swine flu virus may have come from Ohio.
References:
- Vincent, A., Swenson, S., Lager, K., Gauger, P., Loiacono, C., & Zhang, Y. (2009). Characterization of an influenza A virus isolated from pigs during an outbreak of respiratory disease in swine and people during a county fair in the United States Veterinary Microbiology DOI: 10.1016/j.vetmic.2009.01.003
- Yassine,H.M., Zhang,Y.J., Lee,C.W., Byrum,B.A. and Saif,Y.M. 2008. Genetic Characterization of Triple Reassortant H1N1 Influenza Viruses from Pigs in Ohio, unpublished. Influenza A virus (A/swine/Ohio/24366/2007(H1N1))