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How to detect a Man-Made Biothreat

New, high-quality products transmissible strain of influenza emerges. Pesticide-resistant insects can decimate large areas of crop crops. A patient winds up in the emergency room with a bacterial strain that doesn’t respond to any available antibiotics. Natural evolutionary changes between pathogens and pests could lead to any of these situations. But as genetic engineering gets cheaper and easier, it’s becoming increasingly plausible that they might one day be the product of deliberate manipulation.

These potential dangers are being guarded by the US government funding tests that detect bioengineered organisms in their early stages of development. This effort was made public by the Intelligence Advanced Research Projects Activity (or Iarpa) of the Office of the Director of National Intelligence. David Markowitz (the Iarpa manager) announced in an October livestreamed update, that both platforms created under the program could identify bioengineering at 70% accuracy. “We simply never know what sample is going to come through the door in a government lab, and we need to be prepared for anything,” Markowitz said during the news briefing.

The Draper platform, which is located in Cambridge Massachusetts, allows for quick handheld testing that detects engineered genetic material using a tiny chip. Ginkgo Bioworks in Boston developed software that employs machine learning to recognize engineering in DNA data from specimen organisms. (The companies haven’t yet published their results in a peer-reviewed journal, and their platforms are still in development.)

Crops and animal feed are already widely screened to determine the presence of genetic traits that can’t be found in nature or created through conventional breeding. To determine if bioengineered DNA exists and how much, scientists use a technique called PCR (polymerase chain reaction). When it comes to food labeling, scientists usually know what genetic change they’re looking for. There is no universal tool that can detect engineered genetic material found in bacteria, viruses or any other organisms.

The only way to detect bioengineering was manual analysis. This is tedious and laborious. Through a process called sequencing, researchers can generate a readout of an organism’s entire genetic code: a series of As, Cs, Gs, and Ts, or bases, which make up the building blocks of life. Each microbe, every animal and each human have a different arrangement of these letters.

To determine whether an organism’s genetic code has been tinkered with, scientists need to know what its genome—and those of its close relatives—normally look like. This allows them to search for anomalies.

At least half a dozen methods can manipulate DNA. A conventional method involves adding a gene from one species to another—usually for bioengineering crops. Chunks of DNA can also be moved from one part of an organism’s genome to another part, a type of change called a translocation. The Crispr method of gene editing can be used to delete large chunks or DNA. This is an option that has been explored to help people with certain diseases and improve the quality of animals and plants bred to human consumption. Older editing techniques, such as zinc finger nucleases and Talens, have also been used for these purposes but haven’t been as successful as Crispr.

These processes can leave bioengineering signs. For example, scientists can tell if a gene has been added or moved by comparing that organism’s genome to a reference sample. When using Crispr, deletions sometimes turn up in other parts of the genome that look like the targeted section, but aren’t. Talens and zinc finger nucleases also have a tendency to produce these “off-target” effects. Radiation can cause DNA mutations that are traceable if used with care. 

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