In the wake of a 1976 swine flu outbreak that began and ended with soldiers at Fort Dix, New Jersey, virologist Nancy Cox was a postdoc at the U.S. Centers for Disease Control and Prevention (CDC). Today, Cox heads CDC’s influenza division, which has put her at the vortex of the response to the current H1N1 swine flu outbreak. She is also helping to draw up research plans to better understand how this particular swine flu virus has managed to transmit so well in humans and what it does to the human body.
Cox has been at the storm’s center in more ways than one: On 23 April, the day she learned that the unique H1N1 first found in the United States and identified by CDC was also spreading in Mexico, lightning struck her house and all but burned it to the ground. Still, on Mother's Day, 10 May, Cox spoke with ScienceInsider at length about the studies under way at CDC. She explained how scientists there are probing autopsy tissue, immune systems of people who received the swine flu vaccine in 1976, older cases of swine influenza infecting humans, and how currently infected people handle the infection. CDC researchers are also trying to develop improved diagnostics for this influenza A (H1N1) and to assess the potential value of seasonal vaccination against this strain more carefully, as well as the virus's ability to dodge antiviral drugs. Cox says the propensity of a given influenza virus to combine with its relatives and create a new strain altogether—this one is a “triple reassortant” of human, pig, and bird—may have a silver lining, as it could pick up genes from a relative that our immune systems have met and know how to defeat.
This is a condensed transcript of the interview, edited for clarity.
Q: What are the top priority research questions for you and your group?
N.C.: We’ll be looking at animal models and also autopsy tissue from deceased patients who’ve had this disease to look at the pathogenesis.
Q: What specifically will you look at?
N.C. : We’ll compare the picture you see in the lungs of infected people with this virus with pictures of lungs of people who’ve died from seasonal influenza to see if there are any differences, and also to see if there is virus in additional tissues where you don’t normally find it in individuals who’ve died from seasonal influenza.
Q: Is there any evidence from the 50 prior cases reported in the literature of swine influenza in humans that different lung compartments are infected than in human influenzas?
N.C.: There’ve been so few deaths in those cases and no autopsies that I know of. There are additional cases. We just had a [The] New England Journal of Medicine article with 11 cases, and a number of unpublished cases we have at CDC from the past. But they also, by and large, weren’t that interesting.
Q: You’re also looking at antibodies in the blood from people vaccinated in 1976 against that swine influenza. What exactly are you looking for?
N.C.: We’ll be looking to see if there’s cross-reactivity in antibody from people given the swine flu 1976 vaccine with the current virus.
Q: You’re looking at their antibody today or stored samples?
N.C.: These are stored samples. We do not have the ability to trace the 45 million people who got vaccinated.
Q: You could probably find 100 of them.
N.C.: Well, I was one of them. I was a brand-new postdoc here at CDC and of course I volunteered.
We would expect that antibody induced by the swine influenza vaccine would have waned over the years, but there would be memory there. That question is one of scientific interest—and of course of interest if you were involved in the swine influenza vaccination campaign of 1976—to see if there is some residual benefit. With respect to our current response, we wouldn’t say, "OK guys, if you had the 1976 vaccine, you don’t get the vaccine for this one," assuming it’s developed.
Q: Are you suggesting you might see some level of protection in that older group that received the vaccine 33 years ago?
Q: Although early studies suggested that the seasonal vaccine doesn’t provide any protection against the new H1N1, are you looking at the possibility that it might fail to prevent infection but still lessen the severity of disease?
N.C.: We’re looking very, very carefully at panels of serum from individuals who have received different seasonal influenza vaccines, from different manufacturers and from successive years. What we do see is that the older you get, the more likely you are to have what we call cross-reactive antibody with these new viruses. We’re not saying this is protective antibody. But we’re looking very, very carefully at these data.
We’re trying to do the spectrum of age groups that you would need in order to make recommendations about use of seasonal vaccine. What is absolutely clear and confirmed by many groups is that for children 6 months to say 9 years of age, there is no cross-reactive antibody prevaccination or postvaccination from the seasonal influenza vaccine.
Q: Is there any evidence that anyone in Mexico or the United States who has had severe disease has been vaccinated?
N.C.: All the teams are looking very carefully at this. You would be surprised how difficult it is to follow back and find out whether a person is vaccinated. Some people think we should be able to snap our fingers and have this data. And we don’t.
I want to make sure before I give you an answer that I go through the latest data I have, and I’ve been working on other emergent issues.
Q: I understand. I can’t imagine what those would be.
N.C.: You wouldn’t want to know.
[On 13 May, Nancy Cox said CDC knew the vaccination status of 40 people hospitalized because of a confirmed H1N1 infection. Of these, nine reported having received the seasonal flu vaccine, but seven had underlying medical conditions that could have predisposed them to severe disease from influenza. "We're really not able to draw conclusions about vaccine effectiveness," she cautioned.]
Q: Shortly after the new strain was detected, CDC developed and distributed a test that uses the real-time polymerase chain reaction (PCR) assay to detect it. But it’s not the ideal rapid test, is it?
N.C.: No, it’s not. It takes 3–4 hours to get an answer with the real-time PCR.
Q: There are rapid tests on the market now. What are their limitations?
N.C.: All of the rapid tests that are commercially available now only you tell you if it’s influenza A or B or just flu. And there’s a variability among the commercially available rapid tests to do that. Some of those commercial, approved rapid tests have become less sensitive in picking up seasonal influenza A viruses, and furthermore, some of them appear to be even less sensitive in picking up this new virus as an influenza A.
Q: But how would you use these since they don’t subtype at all? You can’t tell that it’s this new H1N1.
N.C. : No, but in the face of an outbreak where you have very high attack rates, say in a school, you could use those rapid tests to determine, yes it’s flu A we’re having here, and you would be able to take specimens from a subset of those kids and send them in to the state health department to get a diagnosis with the real-time PCR.
Q: That helps explain what happened in Mexico.
N.C.: Exactly, exactly. Because they were using standard, available tests, and immunofluorescence tests, and of course they were not able to determine what it was because there’s just not the sensitivity. Now that they have the real-time PCR assay going, they’re able to test a lot of specimens.
Q: What about looking at how much virus infected people produce, the viral shedding studies? What are you doing and what do you hope to learn from them?
N.C.: We’d like to know how long people might be infectious. So we’re looking at both the amount of virus and the duration so that we can try to figure out the period during which people will be able to transmit the virus.
Q: And what’s the average for influenza A?
N.C.: It varies by population group, and that’s what makes this so difficult. Children shed higher titers of virus for longer periods of time. Immunocompromised individuals shed higher titers of virus for what can be very extended periods of time. Normal, healthy adults probably shed virus for 3 or 4 days.
Q: What about kids?
N.C.: Kids can shed virus 10 days or longer. But virus shedding doesn’t equal transmission. You have to be shedding large enough amounts of virus in order to actually infect somebody.
Q: How do you test for viral shedding? Is it a nasal swab done every day? It seems complicated.
N.C.: It is complicated. You have to have serial swabs and try to do semiquantitative PCR or plaquing studies so that you’re actually measuring quantities of virus. And it’s difficult to establish a standardized way of taking the samples so that they’re equivalent every day.
Q: And you don’t have Marcus Welbys going door-to-door visiting people who have flu. How do you do it? Are sick people coming in?
N.C.: We have some field teams out doing these studies, and they’re very difficult to do. It’s difficult to find infected people willing to do it and difficult to put these studies in place. But they are important, and the National Institutes of Health is working on natural history studies as well. And you’re more likely to do these kinds of studies for the more severe patients, for hospitalized patients.
Q: This H1N1 does not have the genotypic mutations known to cause resistance to drugs that inhibit neuraminidase [the "N" in H1N1]. But have you grown the virus in cultures and looked to see whether any isolates might still have resistance to these drugs, the so-called phenotypic test?
N.C.: With the neuraminidase inhibitors, we don’t know the full range of mutations yet that can confer resistance. So to be sure we don’t miss anything, we do the phenotypic test.
Q: Have you seen any isolates yet that are resistant?
Q: It’s inevitable in some people’s minds that we’re going to see coinfections with this new H1N1 and other "seasonal" influenzas, including the human H1N1 now in circulation that is resistant to neuraminidase inhibitors. Could they reassort such that the new strain develops resistance to the drugs?
N.C.: Coinfections occur with enough frequency that we could very well have emergence of an H1N1 virus with the seasonal N1, which is resistant, and the hemagglutinin [the “H”] from this new virus. But the population would have some antibody against that seasonal N1 virus that could moderate the severity of the infection, providing some measure of cross-protection against disease.
Q: So reassortment could have an upside as opposed to the doomsday scenario that that the current strain could acquire resistance to all drugs. Have you detected any coinfections yet?
N.C.: No, we have not. We look very, very carefully for heterogeneity at each and every nucleotide position. So we would be seeing heterogeneity at various nucleotide positions if we were seeing coinfections.
Q: What other studies are you doing that you think are really interesting, even if they’re not as important from a public health standpoint?
N.C.: The various theories of origins of these viruses are being explored in detail. We’re looking very carefully at any additional data that’s entered into the database that might give us additional clues about the intermediates—we’re looking for the missing links. We’re also looking very carefully at how the viruses change once avian influenza viruses are introduced into swine and humans. And we’ve started looking at the hemagglutinin [glycoprotein], and there are some very interesting patterns that we’ll be exploring. We’re doing some structural biology studies looking at what parts of the molecule change, trying to understand from our observations what that could mean in terms of the physiology of the host.
These studies will help us understand not only which viruses are most likely to jump from species to species, but once they’re in a new host, what kinds of changes are likely to occur. That can also help us determine how long the virus has been in that particular host.
Q: I’m interested in the Canadian pig herd. The Canadians apparently haven’t completed the sequencing of the virus in the pig. The assumption that a carpenter working on the farm infected the pig isn’t based on any laboratory evidence, and according to his own description, he only swapped out a few vents at a barn and didn’t have any direct contact with the pigs. It would be interesting to do a phylogenetic analysis of the virus in the pigs and see whether it’s younger or older.
Q: Has that happened?
N.C.: It’s the veterinary folks, the Canadian Food Inspection Agency, they’re doing the sequence analysis, and the last time I talked to my Canadian counterpart on the human side, Frank Plummer, was last Friday and his colleagues hadn’t completed doing the sequence. He thought they would have the complete sequence within the next few days. And he, and everyone else, was really interested in looking at the sequences from those viruses. But from what he knew from his colleagues, the sequence similarity was very great. Of course seeing where it lies phylogenetically is interesting. Could it be a precursor or is it just clearly part of this outbreak?
Q: So you haven’t ruled out the possibility that the pigs were infected first?
N.C.: No, I’m not completely ruling out anything. Until you see the data, you can’t rule anything out.
Q: Given how quickly CDC is able to sequence isolates and post data in GenBank, you seem especially capable of sequencing these viruses. Have you asked the Canadians for this pig isolate?
N.C.: Before this outbreak, we had experience with the triple reassortants from pigs that had infected humans, we had our primers and probes already ready to go. Our machine was already oiled and ready to go. We just had to do tweaking.
But we haven’t requested this isolate because we felt it was well in hand. And human disease is our lane and animal disease is the lane of the U.S. Department of Agriculture (USDA). While we’re working at the animal-human interface and we’re working very close with our colleagues at the USDA, we try to stay in our lane and utilize data generated by those who work on the veterinary health side.
Q: But in this case, you’ve done the triple reassortants that have moved from pigs to humans before. And there’s such a blurring of the lines it strikes me that you’re the ideal place to do it.
N.C.: Correct, correct. We’re always happy, I mean we never refuse samples.
Q: Do you think the outbreak is going to go from the current phase 5 to phase 6, a full-scale pandemic? There was a time when it seemed imminent and everyone said yes, and now it’s, "Who knows, maybe, maybe not."
N.C.: The World Health Organization is looking very, very carefully at spread in Europe to see if there’s sustained transmission and community outbreaks. It’s sort of heading in that direction, but it’s not there yet.
Q: Are you surprised it’s not there yet?
N.C.: What we’ve been able to ascertain is that in the United Kingdom and Spain, they had advanced warning. By the time we had disease it was being disseminated throughout the United States, really spreading quickly. The Europeans were able to screen travelers returning from Mexico or the United States, following up, making sure who had influenza-like illness, putting them on Tamiflu [oseltamivir], putting their contacts on Tamiflu. Some of the countries that have done that and didn’t have very many cases to begin with have been able to really dampen down disease.
Q: I also heard about your house, and that’s horrible timing.
N.C.: If that were my only headache, I would be happy at this point in time.