Posts tagged with genome.
Bacon bites back: a scientist’s fascination with swine flu
I can't help but feel sorry for the pig flu.
I'm passionate about infectious diseases and, ever since "Swine '09: Bacon Bites Back" burst onto the scene amidst a storm of headlines, press briefings and concerned Tweets, I've been consuming news of all things pandemic with insatiable interest, watching with great curiosity as scientists uncover new knowledge about this novel virus on a near daily basis. I wake up every morning and check the case count, cheer when a new batch of genome sequences is released, and chase down all the interviews and press briefings from CDC officials that I can. To use a timely Canadian analogy, I'm pretty much flying the pig flu playoff flag from my car window.
I can appreciate, however, that not everyone shares my rabid interest in swine flu. After all, I am the girl who opted to study microbiology after seeing Dustin Hoffman in Outbreak. I'd secretly hoped that one day my job would take me to Africa, where I'd sport a blue biohazard suit and run nimbly through the jungle, trapping haemorrhagic monkeys with a big butterfly net and, after a flash of brilliant insight, saving civilization from perishing due to systemic visceral organ necrosis.
Most people just want to grow up and have a nice house and fast car, not a biolibrary of primate nasal swabs and fecal samples.
But now we're a week and a half into l'affaire du cochon and I'm realizing that my cuddly-wuddly loveable pig flu - one of the most interesting diseases to register on the scientific radar in recent years - is getting a bad rap. The media focus, with few exceptions, has been on the spread of the disease and its potential impact, and much of what makes swine flu and the pandemic so fascinating has been largely ignored.
Thus, in an effort to improve public perception of influenza A/H1N1, I'd like to present Three Fascinating and Scientific Things You Probably Didn't Know About the Pig Flu.
1. The movement of money is helping to predict the spread of pig flu. For many years, mathematical modeling has been used to simulate and predict the spread of disease in a population. In order to develop a model, however, researchers need data on how humans move at the local and national level. Models based on things like highway systems and population centres are often used, but a group at Northwestern University has modeled H1N1's spread using data gathered from tracking currency. By using data from the wheresgeorge.com bill tracker, they developed a description of human traffic (Lévy flights, superdiffusive random walks, and bi-fractional diffusion equations, oh my!) and have used that in their pig flu projections. Or porkjections.
Their disease models, which are based on the worst-case scenario of no public health intervention, are available at http://rocs.northwestern.edu/projects/swine_flu/. You will doubtless be happy to know that even if we sat back and did nothing, by month's end the U.S. would still only have registered about 2,000 cases of H1N1, about the same number of cases of Beaver Fever they expect to see.
2. This is the first "open-source" outbreak. In early 2003 when SARS broke out, there was a three-week gap between when the virus responsible for it was identified and when its genome was sequenced and made available to researchers. Since then, genome sequencing technology has improved to the point where only three days after the first WHO report of H1N1, 40 viral genome sequences had been completed and released. As of today, over 180 complete H1N1 genome sequences from the current outbreak have been made available. With all of this data, many types of evolutionary analyses are now possible. Keen researchers are exploring these genome sequences and are sharing the results with the community through collaborative wikis and blogs. Other scientists are further blogging and Twittering these sites in a spirit of data sharing and openness that is heartening to see.
A team comprising researchers from Edinburgh, Oxford, and Hong Kong, for example, is publishing its analyses at http://tree.bio.ed.ac.uk/groups/influenza/, where they've reported all sorts of fascinating findings. By using the open-source genome sequence data, they've estimated that the pig flu virus first appeared in September, 2008, and have been able to calculate a statistic that indicates that at the moment, H1N1 isn't spreading very efficiently - only enough to keep itself going at current infection levels.
3. Why the flu is more fatal in Mexico is un gran misterio. To date, there have been 26 confirmed cases where people have succumbed to swine flu, 25 of whom were in Mexico and one of whom was a Mexican who had crossed the border into the U.S. Why haven't any of the other cases been fatal? That remains one of the most fascinating aspects of the outbreak.
The explanation that jumps to the forefront of most peoples' minds is that the Mexican strains must be more virulent than those seen globally. While this is, of course, a possibility, the open-source evolutionary analyses indicate the available Mexican strains aren't too far removed genetically from isolates found in Auckland, New York and Ohio.
Some researchers suspect that pre-existing health factors in the Mexican population might have influenced the disease's outcome, while one leading theory suggests that the increased mortality has to do with the Mexican patients' delays in seeing a physician.
While no one can predict for certain what will happen with pig flu, all indications so far suggest that there's no need for panic. It is, nevertheless, an important reminder that pandemic influenza is a very real threat, with new viruses appearing on a regular basis.
For now, though, just relax, cover your mouth when you cough, and keep washing your hands. And cook yourself up a nice B.L.T. - pigs need all the good press they can right now.
Tagged with
genome,
sequencing,
h1n1,
fatal,
mexico,
mathematical,
flu,
source,
swine,
modeling,
open
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JENNIFER GARDY 
