Until this March, machines at the Broad Institute in Massachusetts were decoding the equivalent of an entire human genome every 10 minutes.
The automated DNA sequencing facility is among the world's largest genomics labs. Its technology descends from that which produced the first working draft of the human genome 20 years ago Friday.
When COVID-19 started taking hold in the United States, scientists at the institute, affiliated with Harvard University and Massachusetts Institute of Technology, realized its genome-reading machines could be repurposed to test patient samples for the coronavirus that causes the disease.
Over the course of two weeks in March, the lab retooled. At a time when testing for the virus has been a critical failing in the U.S. response to the pandemic, Broad says it now has the capacity to run 35,000 tests per day.
Broad is one of several genomics labs across the country that have reinvented themselves as COVID-19 testing centers. Machines that routinely decoded the 3 billion letters that make up a person's genetic blueprint have been quickly brought to bear on the coronavirus' 30,000-letter genome.
"It was just a matter of tweaking the laboratory procedures," said Eric Green, director of the National Human Genome Research Institute, which funds many of these labs. The same machinery analyzes "a much smaller genome, but at a much higher volume."
Moonshot to mundane
In the 20 years since the Human Genome Project produced its first working draft, reading an organism's complete genetic code has gone from moonshot to mundane.
In a White House ceremony on June 26, 2000, President Bill Clinton called the draft "the most important, most wondrous map ever produced by humankind."
The full genome was published three years later. That first map took scientists on three continents 13 years and nearly $3 billion to put together.
Now, one lab can do it in a day or two for less than $1,000.
That advance has been brought to bear on the COVID-19 pandemic.
‘Trivial’
The coronavirus now ravaging the world was unknown until late last year. But Chinese scientists had decoded its complete genome, or sequence, by January 12.
Thanks to technology that made the Human Genome Project possible, "it's actually quite trivial to sequence a given virus," Green said. "And that's why it got done so quickly."
The computing power developed to assemble the complete 3 billion-letter human genome sequence from countless fragments is being used to follow tiny changes in the viral genome as it spreads.
"This gives us an enormous ability to track the virus," said Lee Hood, co-founder of the nonprofit Institute for Systems Biology research center, and co-inventor of automated DNA sequencing.
Researchers can also quickly follow how easily the virus spreads and how virulent it is as it evolves, he added.
Fundamental questions
Scientists are also scouring patients' genomes for clues as to why one patient dies of coronavirus infection while another develops no symptoms whatsoever.
"These kinds of comparative analyses can let us get at fundamental questions like, ‘Why is it that the old are much more susceptible than the young? Why is it that males are more susceptible than females?’" Hood said.
The techniques are mainstream enough that scientists are proposing using them to monitor municipal wastewater for the virus.
"In wastewater are a lot of clues about what are people being exposed to, what viruses are they shedding," Green said. "It is absolutely the fruits of the field of genomics that now can be used" to monitor the environment.
Green added that the size and scope of the human genome project drove a change in the culture of science that's visible in the response to the coronavirus.
When the genome project began in 1990, he said, "team science in biology was not very popular. It was actually frowned upon and almost looked down upon. And sharing data before you publish your paper was almost unheard of. That's completely changed."
COVID-19 research is all about collaborative, open science and data sharing, he said.
"I don't think genomics deserves all the credit," Green added, "but I do think we deserve quite a bit of credit for being the first to really push this and really showcase that and show that it actually benefits everybody."
