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Did the California H1N1 swine flu come from Ohio?
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I just found this very interesting hypothesis put forth by Sandra Porter, a microbiologist/molecular biologist/bioinformatics scientist.
She researched the phylogenetic tree and genome sequence of different viruses and came to the conclusion that the present H1N1 virus in California originated from a 2007 Ohio outbreak.
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?
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.
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. scienceblogs
Please visit the link provided for the complete story.
Interesting stuff, especially since as I understand it, they have found no sick pigs in Mexico. (this is my understanding not a fact).
Wouldn't it be something if this strain actually originated in the US.
She researched the phylogenetic tree and genome sequence of different viruses and came to the conclusion that the present H1N1 virus in California originated from a 2007 Ohio outbreak.
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?
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.
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. scienceblogs
Please visit the link provided for the complete story.
Interesting stuff, especially since as I understand it, they have found no sick pigs in Mexico. (this is my understanding not a fact).
Wouldn't it be something if this strain actually originated in the US.
Wouldn't it be something if this strain actually originated in the US.
weirder things have happened. I started a thread about it starting possibly in the US as well. So far, California seems to be the earliest confirmed date that I can find.
Will have to read up on that Ohio one.
Here in Mexico the news said that the initial infection came from a Canadian tourist so wtf!
I have been hearing more and more from friends in Mexico that the first case in Mexico was in the state of Oaxaca, known for its surfing hotspots, but
that the flu originally was brought to Oaxaca by an American student, from California during springbreak, who stayed at one of these surfing
beaches.
It's still just a rumor though.
It's still just a rumor though.
Mmmm, so the 2007 Ohio is in fact the same strain as the present one ...
In August 2007, about 25 people and 160 pigs developed flu at a county fair in Ohio. Analysis showed they were infected with the same strain -- an H1N1 type containing genes of human, bird and swine origin. WP
Please visit the link provided for the complete story.
In August 2007, about 25 people and 160 pigs developed flu at a county fair in Ohio. Analysis showed they were infected with the same strain -- an H1N1 type containing genes of human, bird and swine origin. WP
Please visit the link provided for the complete story.
A little bit more on Sandra Porter's work.
Emphasis mine, to point out that this is still only a possibility and not a proven fact.
Sandra Porter has a few posts on using digital biology to take a gander at the swine flu that's all the rage. In the first, she uses the NCBI Influenza Virus Resource to see which animals are influenza hosts (the list includes the blowfly, which Porter doubts). Then, she uses the same tool to see which strains have infected certain animals. Next, Porter points out the latest swine flu sequences in GenBank from California, New York, and Texas. She uses that to build phylogenetic trees with that data and more from a 2007 outbreak at an Ohio county fair. They indicate that "the California swine virus is most closely related to a swine flu virus from Ohio" -- though she is refining her work based on feedback on her site. At Aetiology, Tara Smith looks at a new paper on the 2007 Ohio outbreak and Porter's work. "Does this mean the virus came from these Ohio pigs? *Well, no, not necessarily*," she writes, adding that a lot of data is still missing, such as sequences from the Mexican patients and pigs. genomeweb
Emphasis mine, to point out that this is still only a possibility and not a proven fact.
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