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Pathogens watch out, as we embrace the genomic era!

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Posted August 24, 2015

It seems to be a constant arms race – the moment we learn to manage one disease, another one pops up. But the latest technology could help prevent outbreaks before they develop into full-blown pandemics. How?

Image via Pixabay (CC0 Public Domain).

Image via Pixabay (CC0 Public Domain).

Researchers at the University of Birmingham suggest the answer is actually simple enough – genomic sequencing, which is quickly becoming a cheap and portable technology, and… the cloud. An inspirational article summarizing their ideas was published in Genome Biology last month. According to them, the “second revolution” of genomic surveillance will finally help to “shake up public health surveillance”.

So what is so special about the technology that is now at our fingertips, and how can we use it to fight ever-evolving and treacherous bugs? Genetic sequencing, for one, has been successfully employed by epidemiologists for some time now, including the famous 21st century outbreaks – Swine flu pandemic and the Ebola.

However, traditional epidemiology is based on counting disease cases and identifying its culprits post-factum. And while genetic typing can provide a good estimate of what kind of pathogen you’re dealing with, this way one continues to “chase” the outbreak, never quite able to catch up.

Real-time genomic surveillance could change all that completely – for example, a newly emerging virus could be spotted and analyzed inside-out just as soon as a new case is registered. Sequencing could be brought to the field, Instead of going through the painstaking process of collecting-shipping-waiting for results; and, even more importantly, the technology is becoming cheap enough to be employed in resource-limited settings.

Emerging pathogens could thus be identified quickly enough to intervene. It would be easier to predict the disease’ source (e.g. human or animal), geographical origin and learn about the nature of the pathogen itself, thus estimating how might the virus evolve. Same goes for quickly evolving bacteria, such as Salmonella, which affects millions of people every year. Instead of tracing the source after the outbreak has run its course, patterns and spread of infections could be predicted and prevented ahead of time.

But even the most comprehensive genomic data is of little use when viewed in isolation – it’s the “sharing and comparing” that is key to controlling the outbreaks of our age, since often aided by humans themselves, they usually span large geographic regions and include numerous cases.

As the researchers point out, cloud technologies, including Dropbox and Google Drive have now been successfully used in several transnational epidemiological efforts. Moreover, collaborative tools, such as GitHub or Slack help researchers from all over the world to join forces and keep an “open lab book”. Other specialized online tools aid epidemiologists by providing useful visualizations of how the pathogen is spreading, and its evolutionary patterns.

By embracing the available technology, outbreak data from large geographical areas could be pooled and analyzed within days or weeks, making it easier to react in real-time. This would create an unprecedented opportunity to intervene into the outbreak, which could claim thousands of lives.

According to the authors themselves, as the benefits of free data sharing are becoming widely acknowledged, and “cheap as chips” sequencing technologies emerge, “the time is now” to finally get ahead.

Written by Eglė Marija Ramanauskaitė

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