CDC: swine flu strain has genetic roots in U.S.A. 1

(Another hat tip to the increasingly essential Tom Laskawy.)

In an interview with Science Magazine,  CDC chief virologist Ruben Donis essentially confirmed the reading of the current swine flu strain made by New Scientist: that it evolved from a strain that cropped up in U.S. hog farms in 1998. Both New Scientist and Donis emphasize that what we’re talking about is a swine flu—in direct contradiction of the pork industry’s party line. In an interview with me today,  David Warner, director of communications at the National Pork Producers Council, repeatedly attributed the outbreak to “human flu, not swine flu.” He acknowledged that new strain had swine and avian components, but insisted that the human components dominated; and he denied outright that the hog industry had anything to do with it. So that’s the pork industry’s take. Here’s the assessment of CDC’s Donis, as portrayed in this Science interview. 

Q: Is it of swine origin?

R.D.: Definitely. It’s almost equidistant to swine viruses from the United States and Eurasia. And it’s a lonely branch there. It doesn’t have any close relatives.

Q: How about the neuraminidase gene?

R.D.: It has close relatives in Asia. It’s also swine.

Q: The matrix gene?

R.D.: The same as neuraminidase.

Q: So where are avian and human sequences?

R.D.: We have to step back [to] 10 years ago. In 1998, actually, Chris Olsen is one of the first that saw it, and we saw the same in a virus from Nebraska and Richard Webby and Robert Webster in Memphis saw it, too. There were unprecedented outbreaks of influenza in the swine population. It was an H3.

But what about the Asian component? In my interview with the National Pork Producer’s Warner, he suggested that the flu had developed primarily in Asia. The CDC’s Donis isn’t buying that.

Q: What’s the newest part of this strain?

R.D.: Neuraminidase and the matrix are the newest to be seen in North America. They were not part of the team—I talk about flu virus as teams of genes. There are eight players. They have these two new players from Asia.

Q: It suggests a mixing of pigs from North America and Asia.

R.D.: One little detail we haven’t discussed is [that] these Midwestern viruses were exported to Asia. Korea and many countries import from the U.S. Swine flu is economically not such a big deal that many countries don’t check for it.

In other words, the strain stems from from U.S. hog farms in 1998, and has since bounced back and forth between here and Asia.

As Laskawy noted in the above-linked post, Donis doesn’t dismiss Smithfield’s Granjas Carroll operations in Mexico as a possible source of the outbreak.

Q: What do you think about the pig farm in Veracruz?

R.D.: I don’t know the details. They said they had a huge operation and the workers were not getting sick; that’s what the company claims. The only suspicious thing in that story is this is the largest farm in Mexico. The fact that the index case also is from the area makes it interesting.

He does add one thing that will comfort the pork industry.

Q: Do large farms have more swine flu?

R.D.: Not really. Even folks who have 50 pigs have to buy feed and supply from vendors that go from farm to farm, and they don’t wash their boots or whatever. Usually the virus is transmitted very effectively.

Fair enough; but when the 50-herd pig operation gets infected, you’re created 50 carriers for new evolution. When a 15,000-strong hog confinement catches the flu, well, it’s a whole different order of magnitude. Donis ends the interview with the reminder that while the current outbreak seems mild in terms of death rate, medical professionals are doing a lot of finger-crossing.

Q: Is there anything I didn’t ask you that I should have?

R.D.: We all pray this remains sensitive to antivirals. We all hope that vaccines will be developed. The virus doesn’t grow very well in eggs. We hope the virus will improve [the] ability to grow in eggs so we can produce [a] vaccine very quickly so these secondary and tertiary cases can be controlled. In some countries there’s good surveillance, but in others, who knows.

Q: What do you think of this outbreak?

R.D.: This is the first one I’ve seen firsthand as a virologist. The avian influenza outbreak is not comparable because this is unfolding so quickly. This reminds me of SARS. With avian there’s very little transmission. And even with SARS, transmission was far less.

Q: Does this one scare you?

R.D.: I saw figures that do scare you. We’ve received 300 samples from Mexico, and these cover the span of February, March, and April. And you look at flu A, traditionally it’s A/H1 or A/H3 or it’s B up until the end of March. There are two or three cases up to [the] last days of March that are swine. Then in April they skyrocket. So all the cases in the D.F. areas, where most samples came from, it really transmits very efficiently.

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