March 2006 Archives

Chen, et al., ("Establishment of multiple sublineages of H5N1 influenza virus in Asia; Implications for pandemic control" PNAS) report that:

Genetically and antigenically distinct sublineages of H5N1 virus have become established in poultry in different geographical regions of Southeast Asia, indicating the long-term endemicity of the virus, and the isolation of H5N1 virus from apparently healthy migratory birds in southern China. Our data show that H5N1 influenza virus, has continued to spread from its established source in southern China to other regions through transport of poultry and bird migration. The identification of regionally distinct sublineages contributes to the understanding of the mechanism for the perpetuation and spread of H5N1, providing information that is directly relevant to control of the source of infection in poultry. It points to the necessity of surveillance that is geographically broader than previously supposed and that includes H5N1 viruses of greater genetic and antigenic diversity.

And also that:

Our ongoing influenza virus surveillance in southern China shows that H5N1 influenza viruses have been persistently circulating in market poultry populations and also revealed that those viruses were present in apparently healthy migratory birds just before their migration. Genetic analyses reveal that the endemicity of the H5N1 viruses in domestic poultry has resulted in the establishment of distinct regional virus sublineages. The findings of this study demonstrate that H5N1 viruses can be transmitted over long distances by migratory birds. However, viruses in domestic poultry have evolved into distinct regional clades, suggesting that transmission within poultry is the major mechanism for sustaining H5N1 virus endemicity in this region.

Because some migratory ducks sampled in the study have a stronger serological response to an H5N2 probe than to H5N1, it may be that prior infection with a low pathogenic H5 virus has provide some protection against H5N1.  That is, the ducks can carry H5N1 but display no symptoms.  While this is good for those particular ducks, unfortunately it means that rather than dying the ducks can easily transport H5N1 long distances to populations that are completely immune naive for H5 viruses.

The Chen paper also reports the worrisome result that an antiserum raised in ferrets against the current human H5N1 vaccine candidate was strongly reactive against isolates from Vietnam but only weakly reactive against isolates from Indonesia and large parts of China.  Conversely, a ferret antiserum raised against an Indonesian isolate reacted only weakly with isolates from Vietnam and China.  This means the antibodies prompted by the strains from Vietnam don't work against the Indonesian and Chinese strains, and vice versa.  So there is already considerable divergence of the sequence in the wild, and some sequences are not recognized by the present human candidate vaccine.

This becomes even more troublesome with the observation by Chen, et al., of a new genotype in the wild composed of pieces of previously seen ones.  Thus not only are the avian H5N1 strains diverging in the wild to the point that they do not cross-prime mammalian immune systems, but they are also actively swapping parts on time scales that we can now resolve.  It is excellent news that we can actually see what is going on, though not in real time, but this demonstrates that the viruses are clearly able to exchange useful innovations in short time scales, thereby producing new bugs.  The authors conclude from sequence data of the new genotype that, "all eight gene segments of viruses from the Qinghai Lake outbreak in central China can be traced to the H5N1 viruses isolated from migratory ducks at Poyang Lake in southeast China, ~1,700 km distant, indicating that migratory birds can disseminate the virus over long distances."

Chen, et al., conclude the paper with:

The antigenic diversity of viruses currently circulating in Southeast Asia and southern China challenges the wisdom of reliance on a single human vaccine candidate virus for pandemic preparedness; the choice of candidate viruses for development of human vaccines must reflect the antigenic diversity observed across this wider region. Furthermore, antigenic drift observed over time within those H5N1 sublineages highlights the necessity of continually updating the candidate virus chosen for future H5N1 vaccines. These concepts are critical for the control of this pandemic threat.

Which is right on the money, as far as I am concerned.  Except, of course, it would be nice to see more people banging the DNA vaccine drum.

Meanwhile, Stevens, et al., report in an upcoming Science article that, "The hemagglutinin (HA) structure from a highly pathogenic Vietnamese H5N1 influenza virus, is more related to the 1918 and other human H1 HAs than to a 1997 duck H5 HA."  They also study specific mutations to various HA domains to gain insight into potential paths "for this H5N1 virus to gain a foothold in the human population."

The authors come to no specific conclusions about the likelihood of any given mutation, but using a recombinant system do identify a couple of changes that could lead to greater pathogenicity in humans.  A good step forward, though despite all the detailed biochemistry and molecular biology in this paper it leaves me once again feeling like we are still very poorly informed about basic flu virus biology and are simply guessing about the future course of the H5N1 in particular.

Mark Williams' article about the likelihood of bioterrorism, "The Knowledge", is now online at MIT's Technology Review.  I make a brief appearance in the penultimate paragraph.

Most of the article deals with the achievements of the former (we hope) Soviet bioweapons program, and whether new synthetic techniques could be used to reproduce these results in the garage or basement.  I've not much to say about the article.  The text repeats a number of my own observations over the years about the ease of obtaining used equipment, skills, and reagents (in Wired, at Future Brief, and in Biosecurity and Bioterrorism (via Kurzweilai.net), for example).  Williams does explore the issue that increased funding of biosecurity work increases the number of experts and explicitly amounts to proliferation.  Experts are consulted.  I disagree with them.  Enough said.

Technology Review went to the trouble of having Allison Macfarlane, an MIT research associate in the Science, Technology, and Global Security Working Group in MIT's Program in Science, Technology, and Society, give a "rebuttal" to Williams.  Macfarlane begins:

Could terrorists, intent on causing as much harm and societal disruption as possible, use new biotechnology processes to engineer a virulent pathogen that, when unleashed, would result in massive numbers of dead? Mark Williams, in his article "The Knowledge," suggests we should be contemplating this doomsday scenario in the 21st century. Williams's article might make you sleep less soundly, but are the threats real? The truth is that we do not really know.

While most of the rebuttal is well argued, I have to disagree with the last point above: We know the threat is absolutely real, because we know pathogens have been genetically modified in the past.  The question, then, is the timing of the threat becoming imminent.  While it is not technologically challenging to synthesize organisms, or to insert novel genes into viruses or bacteria, it can be technically quite difficult.  That is, the laboratory widgets and reagents necessary to create new pathogens or even to resurrect the 1918 flu are easy to come by, but actually implementing the procedures correctly to produce infectious organisms is quite difficult.  In other words, this activity is still art.  For the time being.

For example, I've explicitly asked around about the difficulty of reproducing the 1918 flu, and responses have varied.  Some people have ignored outright my queries, and others have actively discouraged me from even exploring how hard this might be.  It seems there is a great reticence to discuss this possibility in public.  (I think this is a grave mistake.)  But after prodding people I know who have built RNA viruses in the lab, I would summarize the situation by reiterating that the difficulties lie in laboratory protocols -- skills -- rather than in any technological barrier.  Publishing the 1918 sequence didn't make much difference in this regard: once you know how to make one flu bug you can make any of them.  Worse, you could make a great many flu variants all at once, and let nature sort out which ones are worthwhile weapons.  This isn't news to anyone who has thought about the problem, and the only barrier is trial and effort in the lab/garage/basement/cave.

Thus the threat is very real, and it is probably only a matter of time before the first bug shows up.  How much time, I will not predict.  But I do know we are totally unprepared for naturally occurring threats, let alone the artificial ones that Williams focuses on.  Slowing research will simply leave us ignorant and, when the inevitable happens, struggling to mount even a minimal defense.

"Aaargh Plop", it turns out.  Declan Butler has a story in tomorrow's Nature about the apparent spread of H5N1 among felines.  Evidently, until recently, the "WHO argued that cats are not naturally susceptible to flu, and that even if infected they would not shed large quantities of virus."

But as I observed a few days ago, it is odd that cats are dying in Europe so soon after the virus arrived there.  Dr. Butler notes that H5N1 is not behaving as expected in cats:

...With bird flu it may be different. Later in 2004, Albert Osterhaus's team from Erasmus University in Rotterdam showed experimentally that domestic cats do die from H5N1 and do transmit it to other cats (T. Kuiken et al. Science 306, 241; 2004). And in January this year, the virus was found not only in sputum but also in faeces of experimentally infected cats, suggesting that infected animals may shed the virus extensively (G. F. Rimmelzwaan et al. Am. J. Pathol.168, 176–183; 2006).

It is unclear how these findings relate to cats in their natural environment. But in next month's issue of Emerging Infectious Diseases, Thai researchers describe a cat that died of H5N1 after eating a pigeon carcass. It showed similar pathology to cats experimentally infected with the virus.

It gets worse:

Andrew Jeremijenko, head of influenza surveillance at the US Naval Medical Research Unit 2 in Jakarta, Indonesia, detected H5N1 in a kitten he found near a poultry outbreak in Cipedang, West Java, and tested out of curiosity on 22 January. The virus from the kitten is closely related to recent H5N1 strains isolated from humans in Indonesia: it shares genetic changes found in human strains that are not present in samples from birds.

Interesting.  The standard explanation for the sequence variation would be that the virus propagated at low levels in a cat after it consumed the bird.  But I wonder about another possibility.  Speculation Warning: The flu is very error prone during reproduction, which means that during infection in birds a great many sequences are produced that don't actually survive/reproduce in avians.  But it is possible that a bird can carry a small number of sequences better adapted to mammals that do not proliferate in the bird.  When consumed by a cat, the new sequences might be ready to go in the new host.  That might -- might! -- account for the speed with which the virus started killing mammals in Europe.

Dr. Butler concludes his article with an anecdote about how prevalent feline H5N1 deaths may be in the wild.  The confusion over cat deaths in Europe may simply be another example of ignorance about how H5N1 is actually behaving in nature:

Scientists may just be learning what is already common knowledge among Indonesian villagers. Peter Roeder, a consultant for the UN Food and Agriculture Organization, says locals have an onomatopoeic name for bird flu "that sounds like 'plop', the sound of a chicken hitting the ground when it falls out of a tree. They also have a name for the cat form of avian flu — 'aaargh plop' — because cats make a screaming noise before they fall out of the tree."

The SARS coronavirus came out of nowhere.  It is an example of the speed with which a zoonotic disease can leap to the fore of international attention.  We were completely surprised.  Fortunately, the virus was not quite as virulent as first feared, and it burned itself out before causing greater havoc.  This is an important misconception about the SARS episode.  Yes, the virus was identified and sequenced in a hurry, but all our technology was of little help in responding.  We got lucky.

According to an epidemiological modeling paper published a year after the epidemic:

We conclude that the control of SARS through the use of simple public health measures was achieved because of the efficacy with which those measures were introduced and the moderate transmissibility [R0] of the pathogen coupled with its low infectiousness prior to clinical symptoms[theta].
[Fraser, et al., PNAS | April 20, 2004 | vol. 101 | no. 16 | 6146-6151]

That is, it is quite possible that the much vaunted public health measures used to battle the SARS virus were only effective because the virus wasn't actually that bad.  Not to minimize the death, disease, and the at least US$ 50 billion in economic damage, but it could well have been a lot worse.

This conclusion comes out of a modeling paper, and describes the development of a methodology similar to the one now being used to plan responses to a pandemic flu outbreak.  Unfortunately, there isn't a great deal of data to constrain the model, and as Tara O'Toole and her colleagues at the Center for Biosecurity at UPMC point out (PDF warning), present monitoring and quarantine policy is simply "inconsistent with available scientific understanding of the nature of person-to-person disease transmission."  There is also a distinct question as to how far we should trust the model.  Fortunately, we can look at distinct historical events to figure out whether preparations are on the right track.

Below is a time line of events starting in the fall of 2002, when the SARS coronavirus first emerged.  (Sources:  WebMD, Science, Nature, PNAS, Journal of VirologyNote that while the virus appears to have emerged in November of 2002, it wasn't until February of 2003 that Carlo Urbani saw his first patient.  The diagnosis in November is entirely forensic in nature.  That is, working backwards this seems to be when the virus first jumped to humans.  Koch's postulates, which must be met in order to conclusively link a pathogen and the disease it causes, are not met until the middle of April.  The sequence is then announced at the height of the pandemic, though it isn't published until after most deaths from the initial outbreak have already happened.  Ralph Baric's group at UNC publishes the first paper in October demonstrating control of the virus in the lab, which is a prerequisite to doing any biology, figuring out how the virus works, and developing vaccines.  (Ralph told me at a meeting last week they were ready go to with the paper a few months before it came out.  This delay was probably due to academic publishing BS, as far as I can tell, though it might have gone faster if people were still dying at that point.)  The first vaccine takes another year to test and publish (some of this interval is also due to the dynamics of academic publishing, but the point remains).

Thus the pandemic was basically over by the time we could do any biology and even start to think about vaccines.  But Ralph Baric wouldn't have been able to move as fast as he did in 2003 had he not worked out the packaging strains for the coronavirus reverse genetics system years earlier, published in November of 2000 (Yount, et al., J. Virology).  As it happened, Ralph thought the viruses were interesting, and he put in the time and effort to sort out how to work with them in the lab.  It is only through Ralph's efforts that the rest of us have the good fortune to know as much as we do now about the virus.

What about the next time?  The reverse genetics system for influenza was published in 1999, and we are still trying to figure out how the virus works.  If a flu pandemic hits we might, just maybe, be ready with useful vaccines and antivirals, particularly if the FDA's new flu vaccine licensing rules turn out to be as well thought out as has been reported.  Yet flu pandemics are a near certainty, if only because we have historical examples.  Thus there is a clear motivation to get ready for the next one.  We have a choice about whether to prepare, but the flu is an understood threat.  But what about the next true surprise, the next SARS coronavirus?  And what if it is just a little bit worse than SARS? 

We have to be able to detect the threat, understand it, and respond much more rapidly than is now possible.

CNN is reporting that on Thursday the FDA will announce new draft rules intended to accelerate the approval of new flu vaccines.  This is excellent news.  According to the story, "Eventually, the guidelines could knock one to two years off the time it takes to develop and license a new flu vaccine."

Here is all the good stuff:

...The guidelines make clear there are a variety of approaches to creating vaccines to fight the next pandemic.

The guidelines allow for emergency approval if a completely new super-strain of flu suddenly appears. Or, manufacturers could systematically create and stockpile a library of vaccines against brewing new strains.

They even allow for the possibility of one day vaccinating people against a potential future pandemic strain at the same time they get their regular winter flu shot.

The last point is interesting, because it is an example of explicitly trying to get out in front of a pandemic strain before it appears.  The biggest reason H5N1 is a threat is that humans have never been exposed to a virus like it.  We are "immune naive", which means we have no preexisting antibodies or lymphocytes primed to respond to this particular virus.

Additional interesting policy tidbits:

In the case of a previously approved flu vaccine, manufacturers could tweak the vaccine for use against a new flu strain without having to seek a new license from the FDA, according to the draft documents.

Additionally, a manufacturer could receive "accelerated approval" for a new flu vaccine by performing studies showing that recipients experienced a surge in protective immune-system cells.

This is all good stuff, and comes not a moment too soon.  Okay, it comes a couple of years late.  We're way behind in preparing technological responses either to large outbreaks of infectious disease or to bioterror attacks.  The draft rules are putatively open for comment for 90 days -- if the rules turn out to be as well constructed as CNN is reporting, then everyone should enthusiastically support these proposed changes.

I'll post more when the official documents are released.

As most people have heard by now, H5N1 has reached Germany and is confirmed to have killed a cat (AP via the NY Times).  I think the time scale is of interest here.  The virus has only just reached Western Europe, evidently via migrating birds, and already it has jumped to mammals.  In contrast, there appear to have been few cases in felines in Asia, despite the amount of exposure mammals have had there.  From the AP report:

In addition to the large cats infected in Thailand, three house cats near Bangkok were found to be infected with the virus in February 2004. In that case, officials said one cat ate a dead chicken on a farm where there was a bird flu outbreak, and the virus apparently spread to the others.

I suppose its possible cat deaths are going unreported throughout Asia, but if the AP report is correct then  transmission to cats is very low probability, and I find it odd that the virus is already confirmed to have killed a cat in Germany.  It makes one wonder how the sequence is changing.

Fortunately, there are as of yet no known cases of cat-to-human transmission.  But human exposure to the virus has only just begun in Europe, and the coming months will increase this contact.

All news reports seem to agree that the virus arrived in France and Germany via migrating wild birds.  In an article focusing on the effects of the virus on the French poultry industry, Craig Smith notes in the New York Times that:

...The real threat, many experts fear, may come in the weeks ahead as pintail, garganey and shoveler ducks begin arriving from their wintering grounds in Africa, where the virus has already spread among poultry. The annual migration toward northern breeding grounds is expected to last until the end of May.

Smith also describes how migration patterns have been somewhat unusual this year due to extremely cold weather.  Thus the spread of the virus may be enhanced by changing weather patterns, increasing the likelihood of transportation into areas of the world densely populated by both humans and domesticated animals.  This sort of thing is only going to happen more often.

The AP (via the NY Times) recently picked up this thread with an article entitled, "Scientists See Growing Animal - Disease Risk."  The article begins, "Humans risk being overrun by diseases from the animal world, according to researchers who have documented 38 illnesses that have made that jump over the past 25 years," and winds up:

One explanation may be the recent and wide-scale changes in how people interact with the environment in a more densely populated world that is growing warmer and in which travel is faster and move extensive, Marano said. Those changes can ensure that pathogens no longer stay restricted to animals, she added. Examples from recent human history include HIV, Marburg, SARS and other viruses.

That prospect leaves open the question of what future threats await humans.

''It always surprises us. We think that avian flu will be the next emerging disease. My guess is something else might come out before that,'' said Alan Barrett, of the University of Texas Medical Branch at Galveston. ''It's very hard to anticipate what comes next.''

SARS, in particular, is an excellent example of surprise from nature.  It is also an example of how ill prepared we are for emerging diseases.  It is clear from recent work that if the SARS coronavirus had been just a little more virulent, and if it had spread just a little more before symptoms emerged, then the epidemic would likely not have been held in check by public health measures.  Moreover, it is only because coronaviruses caught the attention of a talented virologist several years before that the community was able to get a handle on the virus as quickly as it did.  More on this in an upcoming post.

(UPDATE, 5 March 06: Ralph Baric is the virologist mentioned above.  Here's the story.)

The NatureJobs section in this week's Nature has a short news piece on science funding, education, and investment in China:

The US National Science Foundation's Science and Engineering Indicators 2006 could perhaps be renamed 'Here Comes China'. The biennial report shows an increasingly international science and technology workforce, with China showing large gains in internal investment in R&D, investment by multinational corporations, and numbers of Chinese nationals earning science and engineering doctorates in the United States.

China has increased its R&D investment 24% per year over the past five years, compared with 4–5% for the United States. This growth, from US$12.4 billion in 1991 to $84.6 billion in 2003, puts the country behind only Japan and the United States. Meanwhile, investment by US-based multinationals into Asian markets outside Japan has more than doubled, from $1.5 billion in 1994 to $3.5 million in 2002, with more than $1 billion going into China alone. Finally, Chinese students earn more US science and engineering PhDs than those of any other foreign nation.

These statistics are impressive, but they tell only one side of the story. What do they mean in terms of jobs and who will get them? The United States, Europe and Japan still produce many PhDs and create a host of jobs. But China is coming on strong. One wild card is whether Chinese PhDs will stay in the United States or return home. While China's PhD production in the United States has increased, PhDs by US white males has dropped from its peak of about 8,900 in 1994 to just over 7,000 in 2003.

It would be premature to say this marks the end of US dominance in science and engineering employment, but it does show that the United States is producing less of its own scientists and may have more difficulty recruiting from abroad as other nations, particularly China, ramp up funding and infrastructure. As the report says, these trends point to a "potentially diminished US success in the increasing international competition for foreign scientists and engineers".

The AP (via the Washington Post) is reporting that the NIH has passed safety trials on a DNA vaccine for the Ebola virus.

From the article:

[Dr. Gary Nabel] and colleagues at the NIH's Vaccine Research Center developed a vaccine made of DNA strands that encode three Ebola proteins. They boosted that vaccine with a weakened cold-related virus, and the combination protected monkeys exposed to Ebola.

The first human testing looked just at the vaccine's DNA portion; the full combination will be tested later.

It will be interesting to see how they go about testing the effectiveness of the vaccine in humans.  There is at present no cure for Ebola, so who is going to volunteer for the test?

The vaccine was reported at a meeting last month.  I'll post additional details as they become available.