In November 2019, Francis deSouza, president and CEO of California-based Illumina, learned from his client-support team based in China that something big in the infectious-disease world might be brewing. Health authorities in Wuhan were seeing cases of a mysterious pneumonia-like illness, and were starting to genetically sequence samples to figure out what they were dealing with—and “scoping out some equipment they needed” to do it at the scale and speed they needed, says deSouza. They turned to Illumina, which makes sequencing machines that can spit out the genetic code of any living thing in hours. In this case, they were hoping that the genetic information would reveal whether the culprit was a known pathogen or something entirely new.
While the orders were being arranged, to speed things along, samples from the first patients in Wuhan were sent to the lab of Zhang Yongzhen at Fudan University in Shanghai. Zhang, an experienced virologist, had in his lab an Illumina NovaSeq, a copier-size machine that is the company’s most powerful workhorse for decoding genomes quickly and accurately. On Jan. 10, his team outed the virus behind COVID-19, posting its entire genome, the equivalent of its fingerprint, on a public genetics database so researchers around the world could use it to develop new drugs and vaccines.
The two months or so from when those first cases appeared to the revelation of the genetic sequence of the virus, SARS-CoV-2, were lightning fast in the scientific world. (It took 13 years to map the human genome; the first draft was completed in 2001.) With the COVID-19 virus’s sequence in hand, scientists at Massachusetts-based biotech Moderna, also relying on Illumina equipment, developed a vaccine to fight the virus in record time—25 days—and were ready to test the shot in people in 63 days, another speed record. BioNTech in Germany wasn’t far behind, and after partnering with U.S. pharmaceutical company Pfizer, it became the first to earn authorization in the U.S. to start vaccinating people—less than a year after Zhang published the virus’s genome.
DeSouza says such a pace, fueled by genetic sequencing, should become routine rather than the exception. The pandemic is providing a stage for demonstrating what such sequencing can do for infectious diseases like COVID-19 as well as other conditions like cancer. “Genomics and genomic epidemiology have emerged as powerful tools in fighting this pandemic,” deSouza says. “The pandemic has brought us into the 21st century, into the era of biology and the era of the genome. We now have genomics being used in a big way in public-health systems, and the role of genomics in infectious disease is permanently changed. I don’t think we are ever going back.”
Illumina is a child of the genetic revolution launched in the late 1990s during the breathless run-up to scientists’ publishing the first draft map of the human genome in 2001. Founded in 1998 (as Solexa) by University of Cambridge scientists to exploit the coming promise of genomics and its myriad uses, Illumina and its initial genetic-sequencing machine didn’t churn out its first commercial genome until 2006—at a cost of $150,000. Over the following decades, its engineers refined the chemical reactions involved in breaking up and reading genetic fragments, providing deeper and more accurate readings more quickly.
Illumina sequencers can now decode a human genome, among the larger genomes around, in about an hour at a cost of $600. “We’ve publicly announced plans to bring that cost down again, to $100 in the near future,” says deSouza, who took the helm of Illumina in 2016 after being recruited from software security company Symantec. “Democratizing access and making sequencing available to everyone helps to deliver the promise of genomics to improve human health, and that’s good business for us.”
Already, any academic, commercial or pharmaceutical lab focused on doing genomics work likely owns one if not several Illumina sequencers. Cancer researchers, for example, are increasingly relying on sequencing to expose tumor cells’ genetic Achilles’ heels so they can be exploited with drugs designed to target those weaknesses. And the ubiquity of the company’s equipment extends to the research world of infectious diseases as well. About 70% of the genomes from the globally sourced COVID-19 samples that have been posted to the public genetic database GISAID were generated from Illumina machines.
Still, when it comes to public health, genetic sequencing isn’t as routine a part of disease management as it should be in the U.S. Most state public-health labs haven’t invested in extensive sequencing capabilities, opting instead to send samples to the Centers for Disease Control and Prevention if outbreaks occur, or partner with local university labs that can run a few samples if time permits.
COVID-19 is changing that. Over the past year, the genetic code spelling out the instructions for SARS-CoV-2 has spawned tests to detect the virus, anti-viral drugs to fight it and vaccines to protect against COVID-19. And increasingly important, the code has served as the foundation for exposing all the ways the virus might be mutating to spread more easily or cause more serious disease.
Genetic information is also proving invaluable in fighting a pandemic in real time. To figure out when SARS-CoV-2 might have started infecting people in the U.S., and how widespread the virus was, in March 2020 Trevor Bedford, a computational biologist at the Fred Hutchinson Cancer Research Center in Seattle, took samples that had been collected for a flu study in the Seattle area and sequenced them for SARS-CoV-2. Not surprisingly, he found that the virus had been circulating in the area for at least six weeks before the first case in the U.S. was confirmed on Jan. 21.
That cemented for public-health officials how useful genetic sequencing could be for making smarter decisions about controlling the pandemic. If, for example, the virus sequences in a given community are slightly different from one another, that would suggest that the infections are entering the region from different places, so restricting travel into that area would help to contain the outbreak. If, on the other hand, most of the cases are similar genetically, it strongly hints that the virus is already spreading within the community and that other public-health measures—such as lockdowns, mask wearing and social distancing—might be more useful.
That’s the promise, but such real-time handoff of genetic information from sequencing machines to policy-makers can’t happen if sequencing isn’t happening at a substantive level. To address that, the Biden Administration invested $1.7 billion in April to expand genetic sequencing for infectious diseases, including creating a system for storing and sharing that information.
But many parts of the world don’t have such resources to purchase Illumina machines, which can run close to $1 million for the most powerful models—not to mention to analyze and interpret the results. “We need global co-operation to come together on a number of fronts,” says deSouza. The first challenge, he says, is creating a global network that scans and shares information on disease-causing pathogens. In 2020, Illumina donated sequencing machines to 10 countries in Africa so health departments could begin sequencing, some for the first time, microbes that doctors collect from patient samples to get a better sense of what is circulating and to identify the especially dangerous pathogens.
That information also needs to be shared with the world. If COVID-19 taught us anything, it is that an outbreak of cases anywhere can soon become a problem everywhere. So in April, Illumina partnered with the Bill and Melinda Gates Foundation and other public and private groups to launch a global pathogen genomics initiative to build genetic-sequencing capabilities in many places where it doesn’t currently exist, beginning with South Asia. The company is committing $60 million for machines and to train experts in the developing world over the next five years. Such a network could sound the alarm if a new virus sparks an outbreak, and the information gleaned from its genetic code could pave the way for quickly developing drugs or vaccines to control it.
As more scientists around the world come to rely on Illumina’s machines, the company’s dominance in the sequencing sector is raising concerns among industry regulators. In March, the U.S. Federal Trade Commission filed a lawsuit to block Illumina’s purchase of Grail, which makes a blood test for detecting cancer, citing monopoly concerns. DeSouza counters that Illumina often sparks innovation and competitive pricing when it enters a space; for example, he says, once the company offered genetic-based analysis for prenatal conditions and for selecting cancer treatments, others followed and drove the price of that testing down.
“We provide tools to clinicians, and they are the ones that make an impact for their patients,” deSouza says. “We provide tools to the world’s smartest researchers, and they are the ones that make the breakthrough discoveries.”