October 2006 Archives

ScienceNOW Daily News is carrying a short piece on the recommendation by the National Science Advisory Board on Biosecurity (NSABB) to repeal a law that criminalizes synthesis of genomes 85% similar to smallpox.

The original law, which surprised everyone I have ever talked to about this topic, was passed in late 2004 and wasn't written about by the scientific press until March of '05:

The new provision, part of the Intelligence Reform and Terrorism Prevention Act that President George W. Bush signed into law on 17 December 2004, had gone unnoticed even by many bioweapons experts. "It's a fascinating development," says smallpox expert Jonathan Tucker of the Monterey Institute's Center for Nonproliferation Studies in Washington, D.C.

...Virologists zooming in on the bill's small print, meanwhile, cannot agree on what exactly it outlaws. The text defines variola as "a virus that can cause human smallpox or any derivative of the variola major virus that contains more than 85 percent of the gene sequence" of variola major or minor, the two types of smallpox virus. Many poxviruses, including a vaccine strain called vaccinia, have genomes more than 85% identical to variola major, notes Peter Jahrling, who worked with variola at the U.S. Army Medical Research Institute of Infectious Diseases in Fort Detrick, Maryland; an overzealous interpretation "would put a lot of poxvirologists in jail," he says.

According to the news report at ScienceNOW:

Stanford biologist David Relman, who heads NSABB's working group on synthetic genomics, told the board that "the language of the [amendment] allows for multiple interpretations of what is actually covered" and that the 85% sequence stipulation is "arbitrary." Therefore, he said, "we recommend repealing" the amendment.

Relman's group also recommended that the government revamp its select agents list in light of advances in synthetic genomics. These advances make it possible to engineer biological agents that are functionally lethal but genomically different from pathogens on the list. The group's recommendations, which were approved unanimously by the board, are among several that the board will pass on to the U.S. government to help develop policies for the conduct and oversight of biological research that could potentially be misused by terrorists.

There has been serious progress recently in developing DNA vaccines for pandemic influenza.  First, Vical just announced (again by press release and conference presentation, rather than peer reviewed publication) single dose protection of mice and ferrets against a lethal challenge with H5N1 using a trivalent DNA vaccine.  Ferrets are seen by many as the best model for rapid testing of vaccines destined for use in humans.  According to the press release:

"We are excited by the recent advances in our pandemic flu vaccine development program," said Vijay B. Samant, President and Chief Executive Officer of Vical. "Earlier this week, we presented data from mouse studies demonstrating the dose-sparing ability of our Vaxfectin(TM) adjuvant when used with conventional flu vaccines. Today we presented data from ferret studies demonstrating the ability to provide complete protection with a single dose of our Vaxfectin(TM)-formulated avian flu DNA vaccine. Our goal is to advance into human testing with this program as quickly as possible, both to provide a potential defense against a pandemic outbreak and to explore the potential for a seasonal flu vaccine using a similar approach."

Mr. Samant will be attending the bio-era H5N1 Executive Round table in Cambridge in a few weeks, along with Dr. David Nabarro, the Senior UN System Coordinator for Avian and Human Influenza.  I'm looking forward to finally meeting these gentlemen in person.

Powdermed is in early human clinical trials for its annual and pandemic flu DNA vaccines in the U.K. and the U.S., and has recently been acquired by Pfizer.  This should provide needed cash for trials, technical development, and perhaps even for building a manufacturing facility for large scale production of their proprietary needle free injection system.  I think it is interesting that a large pharmaceutical company -- a specialty chemicals company, in essence -- has acquired technology that is essentially a chemical vaccine.  I wonder if Pfizer can lend expertise to packaging and DNA synthesis.

Despite progress in the lab and greater funding, there are still significant challenges in getting these vaccines into the clinic.  Here is the DNA Vaccine Development: Practical Regulatory Aspects slide presentation from the NAIAD.  Obviously, lots of work to do there.  And as I have written about previously, it doesn't appear that the FDA is really interested in allowing new technologies to fairly compete, even if they are the best option for rapid manufacture and deployment as countermeasures for pandemic flu.

In other DNA vaccine news, a recent paper in PNAS demonstrated, "Protective immunity to lethal challenge of the 1918 pandemic influenza virus by vaccination."  Kong, et al., showed that, "Immunization with plasmid expression vectors encoding hemagglutinin (HA) elicited potent CD4 and CD8 cellular responses as well as neutralizing antibodies."  Here is more coverage from Effect Measure, which notes that the paper is primarily interesting as a study of the mechanism of DNA immunization in mice against the 1918 virus.

However, if I understand the paper correctly, the authors developed a means to directly correlate the effect of  immunization with antibody production and thereby, "define [the vaccine's] mechanism of action".  This appears to be a significant step forward in understanding how DNA vaccines work.  I interviewed Vijay Samant of Vical by phone a few months ago, and he noted that because animal studies demonstrate complete protection even though traditional measures of immunity do not predict that result, he has a hunch that "tools for measuring immunogenicity for DNA will need to be different than for measuring protein immunogenicity."  Perhaps the results of Kong, et al., point the way to just such a new tool.

An upcoming Nature paper by Micheal Katze, just down the hill here in the UW Medical School, elucidates some of the mechanisms behind the extraordinary lethality of the 1918 virus in mice.  Writing in Nature, Kash, et al., show that:

...In a comprehensive analysis of the global host response induced by the 1918 influenza virus, that mice infected with the reconstructed 1918 influenza virus displayed an increased and accelerated activation of host immune response genes associated with severe pulmonary pathology.  We found that mice infected with a virus containing all eight genes from the pandemic virus showed marked activation of pro-inflammatory and cell-death pathways by 24 h after infection that remained unabated until death on day 5.

In other words, the immune response to infection with the 1918 virus contributed to mortality.  Moreover, "These results indicated a cooperative interaction between the 1918 influenza genes and show that study of the virulence of the 1918 influenza requires the use of the fully reconstructed virus."  That is, you have to be able to play with the entire reconstructed bug in order to figure out why it is so deadly.  And this result gives an interesting context to the recent paper of Maines, et al., demonstrating that reassortant viruses of the present H5N1 and lesser strains are not as fearsome as the complete H5N1 genome (which I wrote about a few weeks ago).  This latter observation has been interpreted in the press as evidence that H5N1 is "not set for pandemic", even though H5N1 is demonstrably changing in nature primarily by mutation rather than by swapping genes.  H5N1 is quite deadly, and it may simply be that the particular combination of evolving genes in H5N1 gives it that special something.

Finally, an upcoming paper in J. Virology demonstrates an entirely new antiviral strategy based on peptides that bind to HA proteins in vivo and thereby prevent viral binding to host cells.  "Inhibition of influenza virus infection by a novel antiviral peptide," by Jones, et al., at the University of Wisconsin, appears to still be in pre-press.

In the abstract the authors state:

A 20-amino acid peptide (EB) derived from the signal sequence of fibroblast growth factor-4 exhibits broad-spectrum antiviral activity against influenza viruses including the H5N1 subtype in vitro. The EB peptide was protective in vivo even when administered post-infection. Mechanistically, the EB peptide inhibits the attachment to the cellular receptor preventing infection. Further studies demonstrated that the EB peptide specifically binds to the viral hemagglutinin (HA) protein. This novel peptide has potential value as a reagent to study virus attachment and as a future therapeutic.

This is just an initial demonstration, but it is extremely interesting nonetheless.  However, because it is a protein based drug, it risks generating an immune response against the drug itself.  It will have to be administered in a way that preserves function in vivo in humans and doesn't spook the immune system.  The last thing you want to do is generate antibodies against a protein vital for human health.

Yet, precisely because it is a fragment of a human protein, it might mean there is a lower risk of generating that immune response, especially if it can be produced in a way that has all the right post-translational modifications (glycosylation, etc).  Though I wonder about variation in the population: various alleles and SNPs.  What if you are given a version of the peptide that differs in sequence from the one you are carrying around?  Would this generate an immune response against the drug even though it is closely related to something you carry naturally, and if so would those antibodies also pick out your allele?  Definitely the potential for bad juju there.  Another example of where personalized medicine, and having your genome sequence in your file, might be handy.  Alternatively, I suppose you could just use your own sequence for the peptide, and have the thing synthesized in vitro for use as a personalized drug.  Sequence --> DNA synthesis --> in vitro expression --> injection.  Hmmm...you could probably already stuff all that technology in a single box...

However it is used, this advance is probably a very long way from the clinic.  It might go faster if they use the peptide as inspiration for a non-protein drug, which, incidentally, the authors suggest near the end of the paper.  Definitely a high-tech solution, either way, but probably the wave of the future.

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 digests information 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...

But seriously folks...it's good news that prizes are being posted for biological technologies.  A couple of weeks ago, the X Prize Foundation announced a $10 million prize for demonstration of "technology that can successfully map 100 human genomes in 10 days."  This is not the first such offer; Nicholas Wade notes in the New York Times that Craig Venter set up a $500,000 prize in 2003 for achieving the Thousand Dollar Genome.  Venter is now on the board of the X Prize Foundation and it appears his original prize has been expanded into the subject of the current announcement.  We definitely need new ways to fund development of biological technologies.

Here's more coverage, by Antonio Regalado in the Wall Street Journal.  It will be interesting to see if anyone can come up with a way to make a profit on the $10 million prize.

The prize requires sequencing roughly 500 billion bases in 10 days.  It isn't possible to directly compare the prize specs with my published numbers since there is no specification on the number of people involved in the project.  If you throw a million lab monkeys running a million low tech sequencers at the problem, you're set.  Except, of course, for all the repeats, inversions, and rearrangements that require expertise to map and sort out.

According to a news story by Erika Check in Nature, the performance numbers cited by 454 Life Sciences appear to be encouraging: "Using the 454 technique, one person using one machine could easily sequence the 3 billion base pairs in the human genome in a hundred days, [Founder and CEO Jonathan Rothberg] says," which is about 3.75 million bases per person per day.  And he is optimistic about progress in reducing costs:  "As the process gets faster, it gets less expensive. "It's clear that we'll be able to do this much cheaper," predicts Rothberg, who says that in the next few years scientists will be able to assemble a human genome for US$10,000."  At the present pace of improvement, this looks to be about 2015, though new technology could always get there sooner.

There seems to be some divergence of expert opinion about where a winning technology will come from.  Writing in Science, Elizabeth Pennisi, notes:

Charles Cantor, chief scientific officer of SEQUENOM Inc. in San Diego, California, predicts only groups already versed in sequencing DNA will have a chance at the prize. Others disagree. "I think it is unlikely" that the winner will come from the genome-sequencing community, says Leroy Hood, who invented the first automated DNA sequencer. And Venter predicts that the chance that someone will come out of the woodwork to scoop up the $10 million is "close to 100%." The starting gun has sounded. 

Indeed.  I had sworn off thinking about new sequencing technologies, but the prize has got even me to thinking...