Microbiologist Celia Alpuche heads the laboratory in Mexico that has become ground zero for the country's outbreak of swine flu. Alpuche spoke to Science yesterday from her office at the Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) in Mexico City.
Many people have raised questions about whether Mexico could have detected this outbreak earlier and contained it before it spread elsewhere. But as Alpuche explains, InDRE had a confusing situation because the virus surfaced in the middle of flu season--and it may not have originated in Mexico anyway. Alpuche also sets the record straight about why it took several weeks to link the outbreak to the first case with symptoms, a 4-year-old boy from La Gloria in Veracruz state. And she frankly describes the limitations of her own lab.
InDRE has worked closely with the Public Health Agency of Canada and the U.S. Centers for Disease Control and Prevention (CDC) to identify the virus as the cause of the outbreak, and Mexico continues to collaborate to test samples of suspected cases. As of 1 May, Mexico had 156 confirmed cases and nine deaths, more than any country in the world. Mexico has identified another 1918 suspected cases, as described in the CDC's Morbidity and Mortality Weekly Report  (MMWR) yesterday, and InDRE is rushing to sort out how many are actually swine flu.
Influenza is caused by two strains, A and B, and several different subtypes that are designated by the two proteins that stud the viral surface, hemagglutinin and neuraminidase, followed by a number. The outbreak is caused by an influenza A virus of the subtype H1N1.
The interview follows after the jump...
Science: There have been many questions about the origin and the timing. When was there an indication that there were an unusual number of respiratory cases?
Alpuche: On April 7, we heard that the National Institute of Respiratory Disease was having unusually severe cases of pneumonia in young adults who were previously healthy. Immediately, we started to get the data around this cluster. We also started to do a retrospective analysis of the influenza data we had.
We looked at all data that we had regarding influenza detection since January up to this month and also to compare to the past season of influenza. In addition to the unusual pneumonia, we started to have rumors there were other cases that were not pneumonia, it was like a respiratory disease, an influenza-like illness.
Science: Did you see anything from your analysis of influenza trends that told you anything?
Alpuche: The first thing that it told us is that we were still detecting influenza in the country, not just in Mexico City. It was pretty much the same as we see every year except it was a prolongation of the flu season. Then we analyzed the subtypes of the strains of influenza, and one of the unusual things we saw was that in this season, we had the first peak in the last part of November and December and another one in February. Over the season, we started having more influenza B than we had the year before.
Science: Which had nothing to do with this outbreak.
Alpuche: Nothing to do with this. It was very confusing. We found that 37% of cases were B and the year before we only found up to 15% were B. Then we looked at data that they have in the influenza surveillance system at CDC to see if were having something unusual. We saw also in United States something kind of similar--a prolonged period of influenza and increases of strain B. So we thought that we were having something related to influenza, and we were still concerned about the pneumonia cases. We went back immediately to look at all the influenza outbreaks we had in the country since the season started to see if this was more related to the prolonged influenza or there was something else we were seeing. We had small outbreaks in some states in the central part of Mexico, Tlaxcala, and then the last outbreak we had was in Veracruz state, in the town of La Gloria, near Perote. That was in the last 2 weeks of March.
Science: Why didn't that trigger concern in the last 2 weeks of March?
Alpuche: It was influenza-like illness, no fatalities and no pneumonia cases. This outbreak was deeply studied with state epidemiologists. The secretary of health of Veracruz did a wonderful job during the outbreak in the last 2 weeks of March.
Science: What capability did they have for typing subtypes?
Alpuche: The influenza, laboratory-based surveillance network in Mexico is using immunofluorescence--that's the screening test, and it's using antibodies against A and B. So that's what the public health state lab is doing.
Science: So they don't have subtype tests and had to refer the samples to you?
Alpuche: Yes. Not immediately, because if there's nothing unusual, they wait to get accumulated cases and then send to the national referral center. One of the interesting things in this outbreak is they were testing, but the onset of symptoms was after 4 or 5 days. The sensitivity of the immunofluorescence test is low after 72 hours. Most of the tests, which were nasopharyngeal swabs, were negative.
Science: You later did more sampling from La Gloria, right?
Alpuche: In the last part of the outbreak in La Gloria, children started having symptoms April 1. They took the samples April 3. They sent the samples to the public health state lab, and they were processed April 4. These arrived at my lab on April 8.
Science: What were the positive ones?
Alpuche: They only identified three influenza strains at the end of the period. One turned out be H3N2. The other was A, but it was not heartening. Here at our lab, we were considering that it could be H1, but it looked indeterminate. To be honest, we were not able to type it. And then we had a B.
Science: The one that you weren't able to type, did you send that anywhere else? Were you concerned that you couldn't type it?
Alpuche: At that moment, we didn't have any information about the untypeable A's that they saw in the California children.
Science: In the surveillance program here in California, if you cannot type it, you send it on to CDC.
Alpuche: That's what we do. Our collaboration center is CDC. We have three different deadlines to do the accumulation of samples to send to CDC during the season. When we had that first indeterminate strain from La Gloria, we were not worried. By that time, the outbreak was controlled.
Science: On April 12, Mexico notified the Pan American Health Organization as per the International Health Regulations about the influenza-like outbreak in Veracruz. Initially, did you think these cases looked like influenza?
Alpuche: Our initial thinking, as we reported according to the International Health Regulations, was that we were having intensification and prolongation of the influenza period. We thought the outbreaks of Tlaxcala and Perote were nothing unusual in terms of the pneumonia. Those were later on, and then we started to consider that there was something unusual.
Science: On 17 April, Mexico started to increase its surveillance for influenza. What triggered the switch to enhanced, active surveillance?
Alpuche: We got a notification of an isolated case, a 37-year-old woman, diabetic, who died because of respiratory disease and pneumonia in Oaxaca. The woman had onset of symptoms April 4. There was no connection at all with Perote. We got samples, and it was a lung biopsy because the relatives didn't allow an autopsy. They intensively investigated the contacts around these deaths. They found some with respiratory diseases but no fatalities. Nothing unusual, okay? They were tested, and all were negative for influenza and other viruses.
Science: When did you first contact Frank Plummer, head of the National Microbiology Lab at the Public Health Agency of Canada?
Alpuche: I contacted him April 17 by e-mail, and he answered immediately. He wanted to know more about this, and we had a long conversation on Saturday, April 18.
Science: Frank told me that he initially didn't think influenza. He thought it would be an unknown pathogen.
Alpuche: Exactly. And we discussed that with Dr. Plummer. In fact, I was the one who called him because I'm the lab person. I met him through the Global Health Security Action Group. And we've been talking about different collaborations, and immediately when we began discussing this and the epidemiology, we wanted to rule out everything we could.
Science: Why did you contact him?
Alpuche: Canada had a lot of experience with the screening of the severe acute respiratory syndrome, SARS, of unknown pathogenesis.
Science: When did you learn of the first two California cases of swine flu that were reported in the MMWR on April 21.
Alpuche: CDC sent me a preprint. I'm not sure exactly when.
Science: When were samples sent to Canada and CDC?
Alpuche: April 21. We asked for help from both at same time. The CDC is my collaborating center in the WHO network. They always help us, doing quality assessment for us, giving us reagents, doing training, transferring technology. But to do shipping for both of them, it was kind of hard. It was a little delayed to get all the permission from the U.S.
Science: Was your decision to send it to Canada also because U.S. authorities were holding up your samples?
Alpuche: No, not at all. I sent these samples to the CDC because they are my collaboration center. That's the way to do it. We get all the help we need from the CDC.
Science: But I think it's important for the United States to learn from this. How long were your samples held up and why?
Alpuche: It was just 1 day difference. I cannot tell you if this is because it is more difficult to send things from Mexico to the U.S. instead of Canada. To be honest, I cannot explain that.
Science: I imagine you were frustrated by the delay.
Alpuche: Yeah, but we knew we were going to get the help that we needed, and we got it. It was just a small difference.
Science: When did you first hear back from Frank Plummer about your samples?
Alpuche: We got the preliminary results April 22. Dr. Plummer got the samples at 3:00 in the afternoon, and by midnight he was calling me to say we had influenza A. Some of the samples I sent him, we knew they were influenza A. That week, we started seeing the A's and we started to change our mind about this influenza B prolongation of the seasonal influenza.
Science: When did you learn that they were positive for a new swine flu virus?
Alpuche: I first learned that it was swine from Frank Plummer; that was in the afternoon of April 23. And later that night Dr. Nancy Cox [of CDC] in a teleconference we had with Mexican experts, we were discussing this and she gave us the preliminary results that we have some swine strains, the ones that just arrived that day at CDC.
Science: What do you think of the criticism that Mexico didn't do enough earlier on to catch this? It's coming from both the Mexican press and the international press.
Alpuche: There's always going to be something to find guilty people in everything. This is a new, unknown virus. We've been growing so much in terms of diagnostics and epidemiological surveillance lately. We still have limitations, that's for sure. We really need to accept that. And we're working very hard to overcome those limitations. We, along with all the health authorities, did everything possible to try to define this as soon as possible.
We're working so hard to try and control this. And we were very open since the beginning. When I received the confirmation from Dr. Frank Plummer, I was immediately in contact with my superior Dr. Mauricio Hernández, and he spoke immediately with Secretary Córdova and he was basically open.
Science: Many laboratories in Mexico City I've visited are very sophisticated. What are the limitations that prevented your lab from identifying the new H1N1? What did CDC and Canada have that you didn't have?
Alpuche: The only place in Mexico doing subtyping is this lab here. We are able to sequence and subtype, but we are overwhelmed with samples of influenza and other things from all around the country. It's a little bit slower than in the U.S. or Canada.
Science: But what were the limits in your lab to isolate the virus and sequence it?
Alpuche: Since this week, we have experts from CDC and Canada helping us to set up a real-time PCR [polymerase chain reaction] technology to test for swine H1N1 directly.
Science: Is your lab the only lab in the country at this point that can do the confirmatory test with the real-time PCR machines?
Alpuche: At this point, yes, but we're working with CDC and Canada to train molecular biologists in different institutions in six different states in Mexico. We have two real-time PCR machines we were able to get immediately--we borrowed one from the company. And now we bought 10 more machines. We are working full-time to speed up the diagnostics.
Science: How many samples do you have waiting to be tested?
Alpuche: Right now, we have a backlog of around 1000 tests that we're rushing to do on time. We're having three shifts of people working, during the morning, afternoon, and overnight.
Science: You have 1000 samples waiting to be tested, but there are nearly 2000 suspected cases.
Alpuche: Not all of the cases that were tested at the hospitals had samples that were referred to us. And not all of the 1000 samples we have are suspected cases.
Science: Are you still sending samples to CDC and Canada?
Alpuche: Yes, we sent more samples to Canada this week, and we are just arranging with the person here from CDC to send more samples to CDC. We want to rule out all these samples we're holding so that we can keep going with the new ones.
Science: A lot of Mexican press and now press outside of Mexico has written about La Gloria and the large pig farm in nearby Perote, Granjas Carroll. There are all these allegations and even conspiracy theories.
Alpuche: I don't know, there are so many rumors.
Science: What about the boy in La Gloria who has received so much attention?
Alpuche: It was mild disease, no problem.
Science: Is it accurate that he is the index case?
Alpuche: We're not sure about that. By the onset of symptoms, he's the first we're seeing in our database, that's all.
Science: What's the onset for him.
Alpuche: April 1.
Science: There have been all these stories of Perote as the epicenter, or the originator. Do you believe that?
Alpuche: We've been asking agriculture authorities, and they ensured us that they didn't detect any problems with outbreaks with animals in these farms near Perote. And the farm is 80 kilometers from La Gloria.
Science: So it's very far.
Alpuche: Even far for a person working there to make the commute. But we are investigating that. We are doing epidemiological surveillance. And we asked the other authorities, and there was basically nothing wrong.
Science: Is there a confirmed case in any employee of Granjas Carroll?
Alpuche: Not that I know so far.
Science: One of the theories is that this originated in the United States or elsewhere and a human came to Mexico, possibly a migrant. The assumption that it was a big pig farm could be very misleading.
Alpuche: Could be. That's the same thought we have. We need more data to prove it. One of the interesting thing is, we're seeing these cases isolated in Oaxaca and Perote, they are well-known for migration. And also the other state that we're seeing several cases now during the active epidemic is San Luis Potosí, and it's like the corridor for migration. It's hard to believe that it's going to be associated with this farm, but I know that the authorities are thoroughly investigated it.
Science: Do you think if this surfaced somewhere other than Mexico it would have been contained, or does influenza just move too quickly anyway?
Alpuche: Considering it was the end of the season, maybe that confused the fact a little that something else could grow, but probably influenza moves too quickly anyway.
Science: The United States detected cases very early, and the United States was not able to contain it. It tells me that the virus is smarter.
Alpuche: Yes, that's for sure.
Science: One last thing. How many hours a night are you sleeping.
Alpuche: [laughter] At the most two.
Science: This has been going on for 2 weeks now.
Alpuche: Yeah, so some days we're getting 2 hours and then a nap of half an hour. And there's Latte. Double shots. Espresso.
Science: Anything you need, anything right now from the international community?
Alpuche: We're okay now in the way we're working, and our collaborators. But at some point if we need it for sure I'll ask. But now, we're okay.