Flu trends

Google has been tracking flu trends for some time by analyzing people's choice of search terms. This method has been very successful and they can usually pick up trends a few weeks before the CDC data. In 2009 a variety of workers from Google and one from the CDC published a paper in Nature describing their technique: Detecting influenza epidemics using search engine query data.

For epidemiologists, this is an exciting development, because early detection of a disease outbreak can reduce the number of people affected. If a new strain of influenza virus emerges under certain conditions, a pandemic could ensue with the potential to cause millions of deaths (as happened, for example, in 1918). Our up-to-date influenza estimates may enable public health officials and health professionals to better respond to seasonal epidemics and pandemics. 
 
The graph above shows, for the United States as a whole, that the peak flu season is usually in February and that we are probably past the peak this year. You can also see how unusual last year was, pandemic years are always different. The big peak in October is from 2009-2010. The same pattern was seen in California except that our peak flu season seems a bit less predictable.

Where's George?

Some of you might already be familiar with Google's flu trends which uses search terms to track the prevalence of flu. Although this might seem like a crude tool it is actually surprisingly accurate and gets the data much faster than the CDC does because it has such a huge volume of data to mine.

The video above shows the results from the project by Northwestern University grad students that uses data from the Where’s George? website that tracks the movement of U.S. paper currency. Again, this surprisingly crude tool is able to amass so much data (they have over 200 million bills in their system!) it has revealed valuable lessons about the movement of people and therefore for the way that diseases like flu might spread. There was an article in the New York Times about the project last year.

Supramap: Predictiong the Spread and Evolution of Viruses

By Annalee Newitz
(Not Me!)
When a pandemic breaks out, disease circles the globe, often leaping from species to species. Now scientists think they can forecast where deadly viruses will strike next, using a new tool that predicts genetic mutation.
Supramap doesn't just track the spread of viruses - it tracks how the viruses are mutating as they jump into new hosts and encounter new medicines. Using Supramap, scientists might be able to stay ahead of the virus mutation curve and figure out when to switch medicines as the microbes adapt and develop resistance.

The Natural History Museum reports on Supramap:

"This tool has a lot of predictive power," says Ward Wheeler, curator in the Division of Invertebrate Zoology at the Museum. "If the movement of a pathogen is related to bird flyways, for example, and those routes are shifting because of something like climate change, we can predict where the disease might logically emerge next."
Operating on parallel programming on high-performance computing systems at Ohio State University and the Ohio Supercomputer Center, Supramap allows any user to input raw genetic sequences of a pathogen's strains and build an evolutionary tree based on mutations. The branches are projected onto the globe with pop-up windows to show how strains mutate over space and time and infect new hosts.

During an earlier phase in Supramap's development, one of the researchers working on it explained how it works:


This week, a paper about Supramap was published in Cladistics. The ability to predict how a virus will mutate over time could be the first step in coming up with a method to stop pandemics in their tracks - or at least, to mitigate the harm they cause by distributing medicines as effectively as possible.
Learn more about Supramap here, and start using it!
via Cladistics [spotted on Natural History Museum]

Send an email to Annalee Newitz, the author of this post, at annalee@io9.com.

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Doesn't this sound like the coolest thing EVER?

Swine flu latest

The President's Council of Advisors on Science and Technology said in a report last week that the virus, although moderate, could infect 30 percent to 50 percent of the U.S. population this year, put 1.8 million people into the hospital and kill anywhere between 30,000 and 90,000 people.
From a Reuters article today.

Also, interesting to see how new technologies are being used this time to track and anticipate the pandemic. The figure below shows how the discussion of 'swine flu' on Facebook is distributed geographically.

Google has been tracking flu trends for some time by analyzing people's choice of search terms. This method has been very successful and they can usually pick up trends a few weeks before the CDC data. Earlier this year a variety of workers from Google and one from the CDC published a paper in Nature describing their technique:
Detecting influenza epidemics using search engine query data.

Malaria map

Worldmapper is an interesting tool that visually depicts geographic data by distorting the size of countries to display the data. They have a number of such maps for diseases - above you can see malaria cases.

Once you have got an idea of how the data is being presented try to imagine what the figure will look like before you click on it. Try the following:

• Cholera cases
  
• Tuberculosis cases
• Rabies deaths

And some older posts of relevance:

• Specicide - Are there species that we should deliberately drive to extinction?
• Malaria control for the 21st century - The Star Wars Mosquito Defense System
  

Epidemiology & Public Health as a Career Option

To be completely honest, I selected EEMB 40 because it sounded like the most interesting course on the Winter 2009 Honors courses list. Soon, I found myself to really enjoy the material, possibly because it has a lot to do with public health, which I personally want to pursue in the future.

For those who might be interested, epidemiology is one of the five core disciplines offered at every CEPH (Council on Education for Public Health) accredited school. There are about 40 of these certified public health schools, including 4 in California (UC Berkeley, UCLA, San Diego States, & Loma Linda). The ASPH (Association of Schools of Public Health) lists possible career titles in the Epidemiology field: Director of Infectious/Chronic Diseases, Outcomes Researcher, CDC Investigator. Public health is very diverse and growing field; those pursuing a career in public health may work in a broad range of sectors.

www.asph.org
www.whatispublichealth.org

A few websites I found to be very helpful. For some reason, I haven't been able to post links on my posts.

Bad tick, no nail varnish for you

When ticks bite they actually secrete a cement like substance that cements their mouthparts in place. That is why they are so hard to remove. Disturbing the tick can cause it to regurgitate material potentially infected with the Lyme disease bacteria into the wound so increasing the chances of infection. Most experts agree that the safest course of action is to avoid the fancy folk remedies involving nail varnish, open flames, or screwing the tick out counter clockwise and go with a straightforward tweezer removal - making sure you grasp the tick as close to the mouthparts as possible and pull smoothly away from the skin. The pictures here are form Cornell's 'Tick Biology for the homeowner' website.

Maps

If you like your data in map form then here are a couple of sites you might want to explore over the holiday weekend.

First up is the Global Atlas of Infectious Disease, I did get quite a few broken links there but there's still some nice maps in the infectious disease section.

The Worldmapper website takes an interesting approach to mapping geographic data. It uses an algorithm that distorts the size of the country to represent the value of interest. The example shown below is HIV prevalence (proportion of people 15-49 with HIV). They have a number of such maps for diseases (eg TB, Cholera, Rabies, Influenza etc) and a whole range of other categories.

ProMed

A little more specialized but worth knowing about is the Program for Monitoring Emerging Diseases (also known as ProMED-mail). Although there are now a number of sites like this one, this is by far the oldest and is probably the largest. Sites such as this make it very hard for any government to remain quiet about a disease outbreak indefinitely. Because of the importance of animal diseases to human health ProMED-mail also reports on emerging animal diseases.

Keep Up Your Knowledge of Disease on the CDC Website

Checked out the Center for Disease Control and Prevention's webpage yet? It is great site that shares various aspects of health concerned information. From everyday healthy living facts to environmental health issues to healthy travel tips to upcoming CDC initiatives and plans and their status in Washington, this site has it all. I was even able to look up exactly how the CDC Funds for State and Local Health Organizations were divided up in the state of California in 2007 (Click Here for the Chart). I was surprised to find that above the $54, 721,262 spent on AIDS and HIV related programs and the $52,577,481 spent on Immunization programs, Terrorism Preparedness and Emergency Response with $79, 458, 396 in funding in 2007 was the category that received the most financial support. Secondly, in comparison to those previously mentioned, the mere $527,948 spent on Heart Disease organizations was also quite a surprise.
The CDC website has much more great information and links so check it out and feed your interest in disease after the end of this course!

Morbidity and mortality

Morbidity and Mortality Weekly Report (MMWR) is a weekly epidemiological digest for the United States published by the Centers for Disease Control and Prevention.

You can sign up to receive it in your e-mail weekly or access the current version and the archives at the website. There's often something interesting there that isn't getting picked up by the mainstream media and when something does hit the media it's a good place to go for the plain facts.

The World as You've Never Seen It

This Worldmapper website re-sizes countries for each area of interest. In the picture above, the territory size represents the proportion of people infected with HIV living there. Use the worldmapper to check out everything from the amount of smoking men to the amount of Cholera cases to the amout of car accidents to the amount of hospital beds. It is a great site that is fun and interesting to fool around on so, go for it! Worldmapper Home

Infectious Disease Podcast

For news and reviews in the realm of infectious disease, check out "Persiflagers Infectious Disease Podcast" (or look in the Science Podcasts section of iTunes). It is provided by a doctor from Oregon (who spells out MRSA rather than calling it mersa), so some of it is a bit 'doctory.' But not surprisingly, a cast from mid-December highlighted several of the themes John touched on in Monday's lecture, and which we will be discussing throughout the quarter. Examples include antibiotic resistance, recent Ebola outbreaks and the virus' possible trend towards lower virulence (that's bad), TB, effects of climate change on Dengue, etc.

This might be a good source of relevant and tangential topics for the blog and for discussion. Plus, when you tell friends what you are listening to, they'll know just how nerdy you really are (or how nerdy your TA is).