By BRETT KELMAN, The Tennessean
NASHVILLE, Tenn. (AP) — Once a week, in an unremarkable brick building in East Nashville, a few dozen samples of the coronavirus undergo a journey that is nothing short of extraordinary.
Lab workers use magnetic beads to strip the microscopic virus of its genetic code, duplicate it millions of times, and then feed a plethora of DNA into a machine that reads it rung-by-rung. Each time the machine recognizes a bit of genetic code, it records a tiny flash of color-coded fluorescent light, amounting to gigabytes of data on an incomprehensible number of flashes that is sent for analysis by a supercomputer in Florida.
When the results come back, the secrets of the genetic code have been laid bare. Each sample of coronavirus can now be identified by a truer name: alpha or gamma or delta or mu.
This is “whole genome sequencing,” one of the newest tools in the Tennessee government’s effort to understand the spread of coronavirus variants and the pandemic overall. Until recently, this kind of detailed COVID-19 testing was largely limited to Tennessee labs run by universities and a few private companies, but the state lab added the capability to sequence the virus on a small scale in July after months of planning, officials said.
Currently, the state lab can sequence only about 75 to 90 COVID-19 samples a week, although it has plans to add equipment that will boost this capacity into the hundreds, deputy lab director Kara Levinson said.
“By doing more sequencing, we’re better able to look at those variants emerging in almost real time,” Levinson said. “So, it’s certainly key to being able to kind of predict where this virus might be heading.”
GENOME SEQUENCING CAN SEE WHAT STANDARD COVID-19 TESTS CANNOT
Genome sequencing, a process that uses powerful computers to map the entire genetic code of any living thing, years ago evolved from science fiction to science fact. Scientists have used the process to identify genes that increase the likelihood of terrible diseases and, through emerging research into the controversial CRISPR technology, make impacting edits to the very building blocks of life.
But the same sequencing technology also serves a more immediate purpose in the battle against the coronavirus. While a standard diagnostic test can detect the mere presence of COVID-19, only genome sequencing can identify and distinguish between variant strains.
Sequencing also potentially can detect the early signs of a new, dangerous variant — much like a ship spotting an iceberg just as it crests the horizon.
This has likely never been more necessary than now. As of Tuesday, Tennessee was reporting more COVID-19 infections per capita than any other state, both in the past week and across the full length of the pandemic, according to virus data published by the Centers for Disease Control and Prevention.
State virus data showed Tennessee is recording an average of 7,400 new infections per day. Only a few days ago, this average was as high as 9,450 infections per day — rivaling the worst days of the winter surge.
Each of those new infections is an opportunity for the virus to mutate. Most of those mutations are insignificant, but sometimes the changes benefit the virus, leading to a worrisome virus variant. So far, no mutation been more impacting than the creation of the delta variant, a more contagious strain that swept the state and the nation.
But future variants could be worse. Another variant potentially could make the virus deadlier or more resistant to vaccination.
A MUTANT NEEDLE IN A GENETIC HAYSTACK
Sequencing starts with the same respiratory samples collected daily at test sites across the state. While most of these samples are used purely to detect whether coronavirus is present, a small portion of some samples is reserved for sequencing at the state lab.
These samples are plucked from particular populations where officials worry mutations are most likely to occur: new clusters, breakthrough infections, pregnant people and infections that are serious enough to cause hospitalization and death.
Once at the lab, the virus’s RNA is extracted and converted to DNA, then amplified millions of times through a cycle of heating and cooling. Making more of the DNA is essential to detecting mutations because, as Levinson explained, if you are looking for a needle in a haystack, it “helps to make multiple copies of the needle.”
The DNA then flows through a sequencing machine in the state lab for the next two days. The data from the sequencer is sent to the University of Florida so a supercomputer — the HiPerGator AI — can lend a fraction of its immense processing power to reconsolidate millions of matches back into results for the original samples.
The vast majority of samples match dominant versions of the virus, like the common alpha variant or the surging delta variant.
“But you can also look at the areas where it doesn’t match up,” Levinson said. “And that’s what helps you kind of track the emergence of new mutations and — eventually — new variants.”
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