But even with the improved accuracy of the platforms, it’s hard to know whether they’ll be able to detect entirely new organisms that scientists have never seen before. Richard Ebright, a molecular biologist at Rutgers University, is skeptical that any technology can definitively identify bioengineered organisms. “There is no technology — no — that can fully and reliably distinguish between engineered and native genome sequences, and never will,” he said. “There are so many ways to manipulate the genome without leaving traces of manipulation.”
This includes a technique called seamless nucleic acid ligation, or slicing, developed more than a decade ago, which uses bacterial enzymes to join DNA fragments. Older methods, such as selective breeding or serial passaging — repeatedly growing viruses or bacteria in new environments over time — are also less likely to leave engineered features, he said.
Gigi Gronvall, a senior scholar specializing in biosecurity at the Johns Hopkins Bloomberg School of Public Health, said the genetic sequence of a new pathogen is not the only factor to consider when determining whether a biological threat has been modified. “If there is suspicion of intentional abuse, attributing it to a particular actor will depend on a lot of evidence,” she said. Factors such as where the new pathogen emerges, who initially infects it, and how it spreads need to be considered. “It’s important to be able to identify these traits that suggest bioengineering, and I hope we can continue to do better. But it’s never going to be a 100 percent picture,” she said.
Of course, not all engineered organisms are dangerous. Companies are engineering bacteria, viruses, plants, animals and human cells to help treat disease or create new foods. Bioengineering testing could help these companies protect their intellectual property, Markowitz said.
But governments are likely to be the main users of the technology. Iarpa has made these platforms available to other U.S. government agencies, Markowitz said. (“I can’t talk about how these tools are currently being used, but I will say that they have been in the hands of a large number of domestic and international partners for several months,” he said.)
He confirmed that, early in the Covid-19 pandemic, Iarpa used techniques from the Felix project to determine that the SARS-CoV-2 virus was not bioengineered. The idea that SARS-CoV-2 was engineered in the lab has since been dismissed outright, but some scientists at the time questioned whether a part of the virus called the furin cleavage site (leading to its high infectivity) was engineered because the Some close relatives of the virus do not have this feature.
Gronvall said the theory has prevailed in part because scientists have limited understanding of the coronavirus. It turns out that other coronaviruses have these sites too. “Until we studied the coronavirus family more and realized our n really low. We’re only sampling a small part of the outside world,” she said. “Now that our field of knowledge is bigger, it’s not that unusual anymore. “
Ultimately, these testbeds could not only detect future engineered biological threats, but also help prevent labs from making them in the first place. “Anyone who wants to be a bad actor, knowing that the tools to quickly detect what they’re trying to do are out there, might think twice,” Markowitz said.