Wanted to draw attention to this wonderful interview with CDC virologist Ruben Donis, chief of the molecular virology and vaccines branch at the U.S. Centers for Disease Control and Prevention, from ScienceInsider. It’s echoes nicely some of the themes I and others have been trying to hit in this swine flu coverage: the mystery about where this virus came from and where it is going; its weird novelty — and the temptations and difficulties in trying to explain that novelty; the huge advantage we have in spotting and studying it because of the "false alarms" from SARS and avian flu; and the need for an aggressive but parsimonious approach to solving the puzzle of this virus so we can think sensibly about how it might behave — and how we should behave.
Donis’s answers (to some wonderfully intelligent questions) recognize all this both implicitly and explicitly, and he seems sharp-eyed in spotting the more solid stones hidden under a murky and roiled surface. (Seems to know where the big holes and slippery slopes are, too.) It’s informative as hell and a delight to read, even if some parts go over your head. It’s nice to know a scientist with such a keen and lively mind — curious, eager, properly skeptical — is parsing this thing.
I’ve tossed a few bits in to give the flavor. You really should go to ScienceInsider and read the whole thing. Takes maybe 5 minutes.
Q: What do you know about this swine flu virus?
R.D.: We know it’s quite similar to viruses that were circulating in the United States and are still circulating in the United States and that are self-limiting, and they usually only are found in Midwestern states where there is swine farming. There’s only one well-documented case where the infection spread from one human to another. What we know is that it is not common that there is sustained transmission in people.
Q: Have you completely sequenced this virus?
R.D.: Yes, 2 weeks ago. Very soon after we received specimens from California and Texas. Hemagglutinin, neuraminidase, and matrix, the three genes that have the most public health interest, were sequenced, and then the whole genome was completed.
[In geographic origin[, 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: 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.
The PB1 gene, that was human. H3 and N2 also were human. The PA and PB2, the two polymerase genes, were of avian flu. The rest were typical North American swine viruses. Those strains were the so-called triple reassortants.
Q: How does it tie to the current outbreak?
R.D.: Where does all this talk about avian and human genes come from? I was describing a fully swine virus. For [the] last 10 years, this has been a fully swine virus. Can you tell I have an accent? I’m a U.S. citizen but I have the roots in Argentina. It’s like me. I’ve been in the U.S. since 1980. I’m a U.S. citizen but I have an accent. [Donis means that yes, it has bird and human elements in it, but those don't seem new to the virus. They've been assimilated but show their echoes, just as his accent shows even though he's now an American.]
Q: Is there anything I didn’t ask you that I should have? [DD note: This is one of the most useful but underused routine q's an interviewer can ask.]
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.
Q: Flu is a seasonal disease that peaks in winter. Maybe this will end in the United States with the end of the flu season.
R.D.: We’re in a good position. The folks in Buenos Aires are in trouble. They’re entering winter now.