Bench Press

In 2003 an unknown virus suddenly emerged in Guangdong China and proceeded to spread rapidly around the world. The SARS coronavirus disseminated around the world via the global air transportation network with stunning efficiency, highlighting one of the unintended consequences of the globe’s vast airline system. After the SARS outbreak, a group at St. Michael’s Hospital in Toronto, took it upon themselves to study the SARS outbreak in detail. The end goal to develop effective strategies to deal with future epidemics. Their project dubbed Bio.Diaspora took a multidisciplinary approach in analyzing air traffic patterns and the distribution of infectious diseases. Their self proclaimed mission:

Understand global patterns of human travel via commercial airlines as a way to predict how emerging infectious diseases are most likely to spread around the world – and consequently apply this knowledge to help the world’s cities and countries better prepare for and respond to global infectious disease threats of tomorrow.

The Bio.Diaspora team believed that not only more applied research into the impacts of global population mobility on public health and security is necessary, but access to quality data on global air transportation and traffic patterns is needed as well. They sought to fulfill this need by:

[D]eveloping a data warehouse for the sole purpose of conducting methodological and applied research on commercial air travel and emerging infectious disease threats. This report embodies rigorous analysis of these data from multiple scientific perspectives – medicine, infectious diseases, public health, health policy, biostatistics, geographic sciences, network analysis, computer sciences, and mathematical modeling.

Their thorough analysis accounted for numerous factors and yielded a report just prior to the emergence of the H1N1 influenza (Swine Flu) pandemic. One of the really interesting parts of the Bio.Diaspora report was the numerous simulations done on potential H5N1 avian influenza transmission from emergence in numerous potential cities around the world.

Click through for interactive version.

The above graphic illustrates the likelihood of importation of H5N1 avian influenza into various areas of the world with an epidemic beginning in São Paulo, Brazil. This caught my eye as it seemingly foreshadowed the H1N1 epidemic. After the emergence of H1N1, the Bio.Diaspora team went back to study the air traffic patterns of the initial stages of the spread (March and April 2009) from Mexico. Running simulations like those from the Bio.Diaspora project’s report they were able to produce predictions based on the flight itineraries (data shown below) that correlated highly with the observed transmission pattern. Their complete analysis is published in the New England Journal of Medicine.

Destination Cities and Corresponding Volumes of International Passengers Arriving from Mexico between March 1 and April 30, 2008.

The Bio.Diaspora project team’s work on both the SARS epidemic and now the H1N1 pandemic illustrate that there’s still much to learn about managing public health crises on a global scale thanks to the highly interconnected nature of today’s cities. It’s a much smaller world now and new tools and ideas will be necessary to deal with future emerging diseases.

(Bio.Diaspora)(Spread of a Novel Influenza A (H1N1) Virus via Global Airline Transportation)

In order to deal with the global outbreak of swine flu effectively, tracking the number of swine flu cases is imperative. Having as much accurate data as possible regarding the epidemic is essential for evaluating what moves the global community ought to start taking to make it through this outbreak. Thus, using quick and accurate tools to evaluate the countless samples  being collected around the world is an absolute necessity. Luckily scientists at the University of Colorado and InDevR, a small biotech in Colorado, may have exactly what the world needs in a microarray chip dubbed the FluChip.

In 2005 Dr. Kathy Rowlen, CEO of InDevR, led a team at the University of Colorado working with the Centers for Disease Control and Prevention (CDC) in developing the FluChip in order to allow labs across the world to quickly distinguish samples between 72 different influenza strains. Her group’s work produced a viable testing platform that produced results in less than 12 hours with impressive accuracy.

Now Dr. Kathy Rowlen and InDevR have licensed the FluChip technology from the University of Colorado. InDevR has arranged to begin testing samples of the swine flu on a M-gene variant of the FluChip while also working on improving the initial design by incorporating new technologies, hopefully making a new assay basic enough that any lab with PCR capabilities will be able to utilize it. Here’s to hoping the FluChip will help us get a better picture of the current state of the swine flu epidemic.

InDevR Press Release:

InDevR, a small biotech company in Boulder, CO, announced today that they have licensed the FluChip technology from the University of Colorado.  The FluChip was invented by a joint team of scientists at the University of Colorado and the Centers for Disease Control and Prevention in an NIH sponsored effort led by Professor Kathy Rowlen.  Rowlen, now the CEO of InDevR, said that InDevR has arranged to test genetic material from the recent swine H1N1 virus on the MChip as well as other versions of the FluChip which are under development.  According to Rowlen “Based on work we conducted a couple of years ago, it appears that the M-gene version of the FluChip will be able to distinguish human H1N1 viruses from the new swine H1N1 virus.  If that proves to be the case, the FluChip will be a much needed and powerful new tool for surveillance since all of the current influenza diagnostics on the market are unable to subtype this virus.” The most popular diagnostic tests for influenza include rapid immunoassays, which are only able to identify the type (A or B) of influenza virus, and reverse-transcriptase polymerase chain reaction assays, which were designed for human-adapted influenza viruses and are not able to identify the swine H1N1 subtype.  State Public Health Laboratories must now send any influenza A viruses that cannot be subtyped using existing diagnostics to the CDC for analysis by genome sequencing or viral isolation.  The CDC must select viruses to analyze since it is not possible to run every sample collected from a large number of Public Health Labs.

The M-gene based FluChip has been demonstrated to delineate human-adapted viruses from non-human viruses, such as the H1N1 virus that caused the 1918 “Spanish Flu”.  “Since the FluChip assay can be conducted within a single day it could be employed in State Public Health Laboratories to greatly enhance influenza surveillance and our ability to track the virus,” Rowlen said.  InDevR will combine the FluChip technology with an innovative detection technology (NESATM), which InDevR also licensed from the University of Colorado and further developed with NIH sponsorship, to make the FluChip assay inexpensive and easy to use in any lab that has basic PCR capabilities.  “Kathy and her team have been engaged with this and similar diagnostic technology for many years,” said Mary Tapolsky, Senior Licensing Manager at the University of Colorado Technology Transfer Office. “CU TTO is excited about this experienced and motivated group developing and commercializing this promising technology.