Scientists can now sequence an entire genome overnight.
This technology has been the key tool in identifying and tracking Covid variants.
Unlocking the Covid Code
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Historians of science sometimes talk about new paradigms, or new modes of thought, that change our collective thinking about what is true or possible. But paradigms often evolve not just when new ideas displace existing ones, but when new tools allow us to do things — or to see things — that would have been impossible to consider earlier. The advent of commercial genome sequencing has recently, and credibly, been compared to the invention of the microscope, a claim that led me to wonder whether this new, still relatively obscure technology, humming away in well-equipped labs around the world, would prove to be the most important innovation of the 21st century. Already, in Church’s estimation, “sequencing is 10 million times cheaper and 100,000 times higher quality than it was just a few years ago.” If a new technological paradigm is arriving, bringing with it a future in which we constantly monitor the genetics of our bodies and everything around us, these sequencers — easy, quick, ubiquitous — are the machines taking us into that realm.
And unexpectedly, Covid-19 has proved to be the catalyst. ....
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Last summer, a few big clinical laboratories, notably Ginkgo Bioworks in Boston, began plans to roll out tests for Illumina sequencers, pending authorization from the F.D.A. Ginkgo, with help from investments from Illumina, as well as a grant from the N.I.H., began building a huge new laboratory next to its current one, where the company would install 10 NovaSeqs. “After we get the big facility built, that’s when we’d be trying to hit 100,000 tests a day,” Jason Kelly, Ginkgo’s chief executive, told me at the time. It was technically possible to sequence many of the positive coronavirus samples, too, he said.
When I asked Kelly what he would do if his capacity goes unused, he didn’t seem concerned. He doubted his sequencers would be idle. “By betting on sequencers as our Covid response,” he remarked, “we get flexibility for what you can use this for later.” After the pandemic, in other words, there will still be new strains of flu and other viruses to code. There will be a backlog of sequencing work for cancer and prenatal health and rare genetic diseases. There will be an ongoing surveillance effort for SARS-CoV-2 variants. An even bigger job, moreover, involves a continuing project to sequence untold strains of microbes, a project that Ginkgo has been involved with in search of new pharmaceuticals. “I think of this as like building fiber in the late 1990s, for the internet,” Kelly said. “Back then, we laid down huge amounts of fiber, then everything crashed.”
But it turned out that a decade after the dot-com crash, optical fiber was essential for the expanding traffic of the web. And what Kelly seemed to be saying, I later realized, was that he would expand his lab because sequencing had to be the future, in all kinds of different ways. There was no going back.
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