Daily Outbreak Forecast

A few days ago, Wired News carried a story by Sean Captain about the Healthmap project, a mash-up of Google Maps and various disease reporting services:

The new Healthmap website digestsinformation from a variety of sources ranging from the World Health Organization to Google News and plots the spread of about 50 diseases on a continually updated global map. It was developed as a side project by two staffers at the Children's Hospital Informatics Program in Boston -- physician John Brownstein and software developer Clark Freifeld.

This follows on Declan Butler's Avian Flu Mashup.  Both efforts encountered significant issues with data formats and parsing the trustworthiness of various data sources.

The Wired News story starts out with this lead: "Web-based maps are handy for keeping tabs on weather and traffic, so why not for disease outbreaks, too?"  And the title is "Get Your Daily Plague Forecast," which. because it is a tad trite, I find rather ironic because a recent PNAS paper demonstrates that, "Plague dynamics are driven by climate variation."

Stenseth, et al., studied the prevalence of Yersinia pestis in the primary host animal, gerbils, as a function of average temperature over 45 years in Central Asia.  They find that ,"A 1°C increase in spring is predicted to lead to a >50% increase in prevalence."  The virus causes bubonic plague in humans, and transmission from rodents to humans is thought to be the main route into the human population.  The authors note in the abstract that:

Climatic conditions favoring plague apparently existed in this region at the onset of the Black Death as well as when the most recent plague pandemic arose in the same region, and they are expected to continue or become more favorable as a result of climate change. Threats of outbreaks may thus be increasing where humans live in close contact with rodents and fleas (or other wildlife) harboring endemic plague.

And as a cheery final note, they conclude that:

Our analyses are in agreement with the hypothesis that the Medieval Black Death and the mid-19th-century plague pandemic might have been triggered by favorable climatic conditions in Central Asia.  Such climatic conditions have recently become more common and whereas regional scenarios suggest a decrease in annual precipitation but with increasing variance, mean spring temperatures are predicted to continue increasing.  Indeed, during the period from the 1940s, plague prevalence has been high in its host-reservoir in Kazakhstan. Effective surveillance and control during the Soviet period resulted in few human cases. But recent changes in the public health systems, linked to a period of political transition in Central Asia, combined with increased plague prevalence in its natural reservoir in the region, forewarn a future of increased risk of human infections.

The combination of climate influences on the prevalence of infectious disease, documented climate change over the last few decades, and the rise of megacities is something we definitely need to watch.

And all this time I was so worried about the flu...

Avian Flu Catchup, 20 Sept 06.

Here are some comments about the GSK adjuvant announcement, the expansion of vaccine candidates by the WHO, H5N1 evolution in the lab and in the wild, and sequence data sharing.

GlaxoSmithKline announced recently that through the use of a proprietary adjuvant they have dramatically reduced the amount of egg-grown vaccine required to produce a decent antibody response in humans. 

A news story at CIDRAP explains that, "The GSK vaccine was made from an inactivated H5N1 virus collected in Vietnam in 2004, according to Jennifer Armstrong, a GSK spokeswoman in Philadelphia," and then notes that, "It is uncertain, however, how effective the vaccine would be against H5N1 strains other than the one it was made from. [Albert Osterhaus of Erasmus Unversity in the Netherlands] told the AP, "This vaccine will only give protection against this particular H5N1 strain and possibly other strains.""

This last statement may be true, but in my view it may also give false hope.  Aside from criticisms others have raised about GSK announcing science by press release, instead of waiting until a publication is ready, or alternatively just releasing the data, we already know that there are H5N1 variants in the wild that kill humans but don't cross prime immune systems.

In response to this development, the WHO recently advised work begin on vaccines based on clade 2 isolates from Indonesia.  (Here is CIDRAP's take, and here is the original WHO announcement.)  Note that this does not mean we will immediately have vaccines in production against these isolates; as far as I know the reference vaccine is still solely based on the original Vietnamese isolate.

As is fairly widely understood at this point, it is not at all clear that vaccines made from either the Vietnamese or Indonesian isolates will protect humans against potential pandemic strains that arise in nature.  Some effort at discerning the threat from certain potential strains was reported in PNAS in early August.  A news story in Nature describes the results with the headline, "Bird flu not set for pandemic, says US team" (subscription req.).

I find that headline very confusing, because the work in question has very little to do with whether H5N1 is "set for [a] pandemic."  Instead, the research explored the effects on ferrets of a exposure to a small number of recombinant viruses consisting of components from H5N1 and H3N2.  The text following the headline is clearer: "The scientists who conducted the work, at the [CDC], say it suggests that the H5N1 virus will require a complex series of genetic changes to evolve into a pandemic strain...  The study [does not] address whether H5N1 could evolve into a pandemic strain by accumulating mutations."

In fact, only very limited conclusions can be drawn from the paper in question, "Lack of transmission of H5N1 avian-human reassortant influenza viruses in a ferret model" (Mains, et al., PNAS, vol 103, no 32).  The first and last paragraphs of the discussion section show the authors are relatively circumspect in interpreting the data:

If H5N1 viruses acquire the ability to undergo efficient and sustained transmission among humans, a pandemic would be inevitable. An understanding of the molecular and biologic requirements for efficient transmissibility is critical for the early identification of a potential H5N1 pandemic virus and the application of optimal control measures. The results of this study demonstrate, that unlike human H3N2 viruses, avian H5N1 viruses isolated from humans in 1997, 2003, or 2005 lack the ability to transmit efficiently in the ferret model. Furthermore, reassortant viruses bearing 1997 avian H5N1 surface glycoproteins with four or six human virus internal protein genes do not transmit efficiently in ferrets and thus lack the key property that predicts pandemic spread.

Although these findings do not identify the precise genetic determinants responsible for influenza virus transmissibility, they provide an assessment of the risk of an H5N1 pandemic strain emerging through reassortment with a human influenza virus. Our results indicate that, within the context of the viruses used in this study, H5N1 avian-human reassortant viruses did not exhibit properties that would initiate a pandemic. Nevertheless, H5N1 viruses continue to spread geographically, infect a variety of mammals, and evolve rapidly. Therefore, further evaluation of the efficiency of replication and transmissibility of reassortants between contemporary H5N1 viruses and circulating human influenza viruses is an ongoing public health need. The ferret transmission model serves as a valuable tool for this purpose and the identification of molecular and biologic correlates of efficient transmissibility that may be used for early detection of a novel virus with pandemic capability.

It is certainly true that this sort of work is vital for figuring out how influenza works, and in particular vital for trying to sort out how reassortant viruses arise, how they change during passage between animals, and how they kill mammals.  Reassortment was historically important in some flu pandemics.  However, the genetic changes seen in nature in the present H5N1 outbreak appear to be solely due to mutation.  In particular, a cluster of cases in Indonesia in April and May -- the first clear example of human-to-human transmission of H5N1, according to the WHO -- allows tracking sequence changes between viruses that infected eight family members.

In "Family tragedy spotlights flu mutations" (subscription req.), Declan Butler writes that;

Viruses from five of the cases had between one and four mutations each compared with the sequence shared by most of the strains. In the case of the father who is thought to have caught the virus from his son -- a second-generation spread -- there were twenty-one mutations across seven of the eight flu genes. This suggests that the virus was evolving rapidly as it spread from person to person.

[While] many of the genetic changes did not result in the use of different amino acids by the virus...experts say they cannot conclude that the changes aren't significant. "It is interesting that we saw all these mutations in viruses that had gone human-to-human," says one scientist who was present at the Jakarta meeting but did not wish to be named because he was commenting on confidential data. "But I don't think anyone knows enough about the H5N1 genome to say how significant that is."

So there is considerable mutation occurring, even between viruses present in different family members, and we don't yet know enough about H5N1 in humans to say whether this is significant with respect to evolving into a pandemic strain.  But even more interesting, there are so many differences between the viruses that they look like different clades.  Again, from Dr. Butler:

Elodie Ghedin, a genome scientist at the University of Pittsburgh School of Medicine in Pennsylvania, says she's surprised that the virus from the father had so many mutations compared with others in the cluster, apparently arising in just a few days. "I have a hard time believing that the father acquired the virus from his son," she says, adding that the nine mutations in one gene in the father's virus are almost identical to those in viruses isolated from human cases in Thailand and Vietnam in 2004.

One possibility is that the father simply caught a different strain of virus from birds, although other mutations in his virus are similar to those in the strain isolated from his son. Or perhaps the virus from the son reassorted with another flu strain circulating in his father at the time, Ghedin says.

Perhaps, but it would seem that if the father was also carrying a virus from Thailand or Vietnam that there should be signs in birds or other humans.  I was unable to find out whether the father was in a position to pick up a virus from another clade, which would be a good check on the likelihood of reassortment.

Dr. Butler goes on to note that a simple lack of information is a significant factor in the slow progress:

Part of the reason the picture is so unclear, say virologists contacted by Nature, is that the continued withholding of genetic data is hampering study of the virus. None of the sequence data from the Indonesian cluster has been deposited in public databases -- access is restricted to a small network of researchers linked to the WHO and the US Centers for Disease Control and Prevention in Atlanta, Georgia.

Fortunately, this has changed and the Global Initiative on Sharing Avian Influenza Data (GISAID) is now in place.  I'll have something more later on the sharing plan after I digest all the information.  It looks like a nice step forward, but, as always, we'll have to see what comes of it.

PowderMed Files for Human Testing of H5N1 DNA Vaccine

Here's a recent story from Reuters about PowederMed's vaccine.

The first-time-in-man clinical trial will be conducted at aclinical research unit in London and will examine the ability of a vaccine based upon the Vietnam H5N1 avian influenza strain to protect against a potential pandemic form of flu.

Confusion Over Indonesian H5N1 Outbreak

It seems there is a profusion of bad information about the present Indonesian H5N1 outbreak.  Over the last week, The New York Times has reported conflicting statements from the World Health Organization about whether the cluster of cases was caused by human to human transmission.  Somebody needs to make up their mind about when to talk to the press, and who to let speculate about the science when they obviously have no idea what's going on.  How are we supposed to have any confidence if they keep shooting from the hip before solid evidence is in hand?

As important as whether there was confirmed human to human spread is the issue of how the sequence is varying.  I wrote earlier this week about reports that changes in the human sequence appeared to put it closer to a feline sequence, but Wired News is carrying a Reuters story in which the WHO states otherwise:

"Sequencing ... found no evidence of genetic reassortment ... and no evidence of significant mutations," the United Nations health agency said in its statement.

I would note now that I'm not sure what Andrew Jeremijenko means by "the closest match we have to the human virus is from a cat virus."  I was unaware there was any distinction observed in the wild between viruses afflicting humans and felines.  But the point is that one agency is saying the virus is changing and may be related to something killing other mammals, while another says there are no mutations and can't make up its mind whether we already have human to human transmission.

People, get your shit together, please.  Don't talk to the press until you know what's going on.  This thing is scary and complicated enough as it is without having to sort through conflicting information from "official sources".

Indonesian H5N1 Outbreak Linked to Cats?

(Sitting in the Synthetic Biology 2.0 meeting, so this will be brief.)

Following up on my earlier reports and speculation (here, here and here) about the role of felines in spreading H5N1:

The Australian Broadcast Company is carrying an interview in which Andrew Jeremijenko, Project Leader of the Influenza Surveillance Studies for a US Naval Medical Research Group, suggests the outbreak in Indonesia may be directly related to infection in cats.

The article, entitled "Failed Indonesian bird flu response concerns experts", by Peter Cave, contains the following exchange:

PETER CAVE: Are you seeing mutations in the virus in Indonesia?

ANDREW JEREMIJENKO: Yes, that's a good question. We are seeing mutations in the human virus. We are not seeing that same mutation in the bird virus. And that's of great concern.

Basically, when you do an investigation of a bird flu case, you should try to find the virus from the human and match it up with the virus from the bird and find the cause.

Now, in Indonesia, the investigations have been sub-optimal, and they have not been able to match the human virus to the poultry virus, so we really do not know where that virus is coming from in most of these human cases.

PETER CAVE: Does it suggest it's going through an intermediary before it's infecting humans?

[Andrew Jeremijenko]: It's a possibility that we can't rule out. I think they really need to do a lot more investigations. So far the closest match we have to the human virus is from a cat virus. So the cat could be an intermediate. We really don't know what's happening yet.

Avian Flu Catch-Up

Changing diapers is definitely a distraction from H5N1, but now the kid is zonked out and I have a chance to catch up a bit.

Chinese Domestic Flu Vaccine Production

Almost a year ago, I examined the implications of the lack of pandemic preparedness in Asia, particularly China.  The April 06 issue of Nature Biotechnology carried a news piece (Pubmed) that basically confirms part of what little I had been able to determine about Chinese domestic flu production capacity.  Not much new in the piece, but at least it allows me to point to a reputable news source instead of merely one of my blog entries.

Avian Flu in Felines

In early March, I was prompted by an AP story to wonder about the implications of a cat killed by H5N1 in Europe as soon as the virus showed up there (see, "Avian Flu as a Harbinger of Zoonotic Diseases").  Soon after, Declan Butler came out with a news story in Nature about this, and recently Nature carried a commentary by Albert Osterhaus and colleagues exploring the issue in more detail (Kuiken, et al., Nature 440, 741-742 (6 April 2006) | doi:10.1038/440741a).  This latter piece takes issue with the bland and unconcerned statements by the WHO and OIE that H5N1 in felines is uninteresting and, more importantly, has no influence on the spread or evolution of the virus.

Kuiken, et al., observe that fatal infections in cats are common in SE Asia and the Middle East, and:

Given the high number of infected cats in these areas, and considering their ability to excrete virus into their surroundings in sufficient quantities that transmission between cats takes place under both natural and experimental conditions (see below), cats could be more than a dead-end host for H5N1 virus.

...Apart from the role that cats may play in H5N1 virus transmission to other species, they also may be involved in helping the virus to adapt to efficient human-to-human transmission.

There isn't any evidence of this, to be sure, but it is a damn scary thought.  It is important to note that there isn't any evidence in part because we really aren't doing a very good job of looking.  Our environmental monitoring for zoonotic diseases is dramatically underfunded.  Bugs that kill humans often come from animals, and we are doing a piss poor job of understanding how and why pathogens make the jump.  (See my post "Nature is Full of Surprises, and We Are Totally Unprepared".)

More Damn Cladistics

The 27 April, 06 issue of Nature has a back-and-forth between Taubenberger, et al., and two groups disputing the assertion that the 1918 pandemic flu virus was avian in origin.  Gibbs and Gibbs assert that the virus was in fact a reassortant previously present in mammals.  If nothing else, they get this right; "In light of this alternative interpretation, we suggest that the current intense surveillance of influenza viruses should be broadened to include mammalian sources."  (The growing awareness of the effects of the virus on felines is evidence we should be doing more to monitor the virus in the wild.  Never mind that of the $1.9 billion recently pledged to prepare for a pandemic, exactly none was pointed towards better monitoring.)   Antonovics, et al., similarly, argue that Taubenberger and colleagues got the phylogenetic tree wrong and that the amino acid sequences of the RNA polymerase genes put the 1918 virus, "within...clades containing strains from other mammalian hosts."  They conclude:

By stating that the high pathogenicity of the 1918 virus is related to its emergence as a human-adapted avian influenza virus, the authors raise the possibility that an emerging avian strain could resemble the 1918 flu. This alarming implication, which is based on misinterpretation of the phylogenetic data, is completely unjustified and could seriously distort the public perception of disease risk, with grave economic and social consequences.

Fair enough, if Taubenberger, et al., have in fact come to the wrong conclusion.  Taubenberger and co-authors give what appears to be a comprehensive hearing to their detractors, and appear to answer the challenge well.  I think the best bit of their argument is as follows:

We have never maintained that the virus entered the human population in 1918: rather, as described earlier, our claim that it entered the human population "shortly" before the pandemic should be interpreted as 'at least several years before the pandemic', as stated in our discussion. The path that the precursors of the 1918 pandemic virus took before emerging in humans in 1918 remains unknown. Phylogenetic analysis on its own cannot definitively resolve the issue. As in previous analyses, we analysed the sequences of these genes for clues about their origins and found that the proteins encoded by the 1918 polymerase genes were avian-like in all cases.

I like this bit in part, of course, because I can understand it.

The argument about the origin of the virus seems half well-founded and well-measured molecular evolution, and half complete hand-waving.  (My interpretation may be influenced by the Cointreau on the rocks I am working on.  This is Uncle Sydney's drink, and I have been hoping it will rub off, though, admittedly, it doesn't seem to be working.  Yet.  Buy, hey, it's fun to try.)  I am frustrated by the cladistics story in part because there is no way to judge the merits of either side of the argument without delving into the details of not only the sequence variation and fundamental virology but also the statistical models used to generate phylogenetic trees.  This, I definitely don't have time for.  Nor, I suspect, does anyone else outside the field.  We simply have to watch the debate and see where it goes.

The real point, of course, is that we don't know where the virus came from.  It is still a mystery and will likely remain so.  Because of the evidence presented by Oxford, et al., I tend to side with Taubenberger.  It doesn't really matter, though.  Regardless of where the virus came from, the lesson today is that since we don't understand what happened before, we are completely unprepared for anything like it that may come in the future, as I have written about before.

More Vaccine Tiddlywinks

Unfortunately, as I briefly alluded in a recent post, the NIH doesn't seem to be doing much to prepare us for future outbreaks.  While the Institute has awarded just over a billion dollars to manufacturers to get cell-culture vaccine production up and running, this is simply a new way to make the old vaccine.  In interviews with those same manufacturers for the bio-era Avian Flu and Economic Impacts of Genome Design projects, they were quick to admit cell-culture production will get vaccines out the door in, optimally, four to five months instead of the six to eight month figure overused when discussing egg-based production.  This is a modest improvement, to be sure, and it is possible that cell-culture techniques can be used to produce more doses.  But this doesn't help make better vaccines.  If we used cell culture to produce the present reference vaccine, we would still be screwed because it seems very likely that the reference vaccine will be next to useless.  Where is the additional funding for alternative, or fundamentally new, vaccine technologies?

A news story in the 27 April edition of Nature offers some slight hope.  In, "Flu-vaccine makers toil to boost supply," Carina Dennis writes that, "More than a dozen groups are developing pandemic vaccines, testing a range of strategies to boost potency and production capacity."  Ms. Dennis follows with the suggestion that moving from split virus vaccines to whole virus vaccines.  That is, using intact virions instead of the standard vaccine in which the virus is disrupted with detergent.  An accompanying map shows worldwide efforts to develop new vaccines, though I note only one subunit project (Solvay) and one surface antigen project (Chiron).  There is no mention of DNA vaccines, either from PowderMed, delivered using gene guns, or from Vical, delivered via intramuscular injection, which I am waiting to hear back about from the manufacturer and from the doc in charge of a recent clinical trial.  Ms. Dennis notes that a study published by Neil Ferguson suggests that, "to curb the spread of disease, vaccinations would need to begin within one to two months of the pandemic starting."  Once again we are back to facing the need for a quick response while equipped with technology that is very slow.  And we have a crappy vaccine stock to start with.

And with that, I am tempted to start ranting again about the need to completely revamp our technological response to infectious disease, which you have all heard before.  So it is time to sleep and dream of better things.  Like changing diapers.

Comments on new FDA rules for expedited development of pandemic influenza vaccines

I'm a bit behind on the blog, having spent most of the last four weeks on the road, battling a norovirus (Yuck.  Don't get this bug  Hey Ralph, where the hell is my vaccine?), doing my taxes, and buckling down in the lab trying to get devices fabricated.  Cool progress on the later, which, alas, has to be disclosed to the University, written up for publication, and a patent application filed before I can discuss it here.  Harrumph.

A great deal has transpired on the influenza front, including news that the current H5N1 vaccine is as useless (NY Times) as predicted, which means that the need for alternative vaccine technologies is now even greater (more on this in a forthcoming post).  But I will start with the FDA's new draft guidelines on accelerated licensing of influenza vaccines, which I briefly addressed at the beginning of March.  The suggested guidelines were officially announced a few days later.  What follows is my take after a quick once over.

Here is how the document (PDF warning) starts off:

This document is intended to provide to you, sponsors of pandemic influenza vaccines, guidance on clinical development approaches to facilitate and expedite the licensure of influenza vaccines for the prevention of disease caused by pandemic influenza viruses.  The approaches apply to "split virus" and whole virus inactivated pandemic vaccines propagated in embryonated chicken eggs, and are also applicable to cell-culture derived, recombinant hemagglutinin-based protein, and adjuvanted pandemic influenza vaccines.  We, FDA, also address live attenuated influenza vaccines. This document does not address influenza vaccines that do not contain a hemagglutinin component.  Current U.S. licensed influenza vaccines are trivalent vaccines approved for the prevention of seasonal influenza illness.  Two classes of vaccines are licensed, "split virus" trivalent inactivated vaccines and a live attenuated trivalent vaccine. (pg. 1)

Beginning on page 2, by the way, is a short and very nice introduction to the biology and history of pandemic influenza viruses.

Here are some interesting quotes from the press release:

The FDA provides manufacturers with clear guidance on developing and submitting clinical data to show safety and effectiveness for new vaccines.  Consistent with the aims of FDA's Critical Path Initiative to get products to market more quickly and to advance the development and use of new technologies, these documents outline specific approaches that vaccine developers may follow.

...In issuing this advice, FDA aims to facilitate manufacturers in increasing the number of doses to ensure that enough influenza vaccine is available to vaccinate each person in the at-risk population. Having additional diversity in our vaccine supply helps enhance the capacity to produce more doses of influenza vaccine and contributes to the nation's pandemic preparedness.

...The release of these guidances is part of the comprehensive effort that FDA is undertaking to work with manufacturers to facilitate the development of vaccines.  Other examples include a recent CBER advisory committee meeting to discuss novel approaches to develop influenza vaccine such as using cell technology rather than eggs, frequent interactions with vaccine manufacturers to provide both scientific and regulatory guidance, as well as CBER's preparation of material for testing the potency of new vaccines, which are made available to manufacturers.

All in all, an exceptionally conservative document, given the magnitude of the problem we are facing.  The recommendations should do very nicely in all circumstances save the emergence of an actual pandemic.

The main problem I have with this announcement is that it appears to be geared towards easing the way for approval and use of particular technologies -- namely vaccine production by cell-culture, split virus vaccines, and specific recombinant protein vaccines -- rather than defining engineering and immunological goals that any given technology should meet to be approved.  For example, PowderMed's DNA vaccine does not appear to fit into the new guidelines, despite arguments the company is likely to make that injecting a plasmid coding for the hemagglutinin is equivalent to injecting the protein itself.  I hope I am wrong about this, because DNA vaccines look to be the only technology that can be used to respond on short time scales to rapidly spreading diseases.

No doubt I will return to this issue as the rules are discussed and developed.

Update on H5N1 Evolution

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.

What is the Sound of a Cat Dying from Avian Flu?

"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 thateven 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."

Nature is Full of Surprises, and We Are Totally Unprepared

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), 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 Virology.)

Note 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.  Future 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, and 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.