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Ginkgo is trying to detect future man-made biological threats

A general view of a lab space in the Ginkgo Bioworks office in Boston, Massachusetts on Tuesday, Sept. 6, 2022.Adam Glanzman/Bloomberg

Synthetic biology firm Ginkgo Bioworks has developed tools that US intelligence agencies can use to detect engineered DNA at scale, a milestone that could better protect the nation from human-made biological threats. The new software could be used to provide an early warning of bioweapons, such as a new deadly bacteria, or a modified virus that thwarts existing vaccines.

As biological engineering becomes cheaper and more accessible, the US government has doubled down on efforts to detect and prevent both accidental and deliberate threats. Through a partnership with the Intelligence Advanced Research Projects Activity, a high-risk research agency within the Office of the Director of National Intelligence, Ginkgo has created software that will help the US determine when biological organisms, such as viruses, plants or animals, have been genetically engineered.


In nature, the genetic code of an organism often changes, sometimes significantly. Covid-19, for example, has mutated several times, making the virus more contagious. But determining whether a genome has been engineered or manipulated by humans has proven to be a difficult task. Existing methods for detecting biological engineering are expensive, slow and have limited use.

“Ginkgo has achieved a major breakthrough for the biodetection community at large,” said David Markowitz, a program manager at IARPA, in a statement. “The ability to detect genetic engineering in complex biological samples has long been a moonshot goal, and this new capability is poised to transform national biosecurity efforts.”

The announcement of the new technology marks the culmination of IARPA’s project FELIX, which stands for Finding Engineering-Linked Indicators, and dates back to 2018. Its purpose was to improve the nation’s detection, identification and response to human-made biological agents that have the potential to cause harm.

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Through the project, Boston-based Ginkgo’s new computational tools, known as ENDAR, or Engineered Nucleotide Detection and Ranking, aim to help analysts identify signatures of genetic engineering in a range of organisms.


“Ginkgo has a core belief in the promise of engineered biology —- a thriving bio-based economy that delivers benefits to society, the environment, and our health,” Jason Kelly, Ginkgo’s chief executive officer, said in a statement. “We care deeply about securing that vision by ensuring that biology is engineered and deployed responsibly.”

Nonprofit engineering firm Draper, which was also contracted by IARPA, developed a lab-based genetic test and tools that help the contextualize DNA-sequencing data that Ginkgo produces, among other contributions to the FELIX project. The technology could also be used for environmental monitoring and food inspection in addition to biothreat detection.

Amid the Covid-19 pandemic, the Biden administration put a priority on improving biosurveillance and security. In September, President Joe Biden signed executive order laying out a strategy to bolster domestic biotechnology and biomanufacturing and secure the US supply chain. The White House is also expected to release its new National Biodefense Strategy imminently, according to people familiar with the matter, who asked not to be named as the details aren’t public.