Nanopore Sequencing at the Institute of Arctic Biology’s Genomics Core lab in Fairbanks
FAIRBANKS, Alaska (KTVF) - We had the opportunity to take a look inside The University of Alaska Fairbanks (UAF) Institute of Arctic Biology’s Genomics Core lab to see the instruments being used in COVID-19 analysis.
It’s cutting edge COVID-19 research, and Dr. Devin Drown explained the science behind viral genome sequencing: what it is, and how it’s done.
(This is part two of a three part series, part one can be found here)
Sequencing the genome of COVID-19 samples is a process of analysis which produces a detailed picture of the virus’s genetic information.
“This virus is an RNA virus, and so that’s one type of genetic code. Humans... our genetic code is DNA -- and so with an RNA virus, the first step to understanding the As Ts Gs and Cs, the letters that make up it’s genome... the first step to understanding that is actually translating that RNA into DNA," said Drown.
One of the technologies to sequence genomes is called nanopore sequencing. Drowns explained, “Nanopore Sequencing I think is quite easy to understand. You have a string of As, Ts, Gs, and Cs, this genetic code. These bits of DNA are threaded through a hole, a nano pore, a small hole. An electric charge is running through that pore, and that charge is disrupted by the DNA running through the pore. That signal as it’s adjusting whether there’s and A, or a T, or a G, or a C, that signal is recorded. We can decode that signal with a computer and figure out ‘ah there was an A going through that hole, or a T’ at a particular time,”
The DNA sequencer used for this process Is very small device, allowing it to be used portably.
“As you can see it literally sits in the palm of your hand. We can plug this device into a laptop, and run the sequencing from the laptop," said Drown.
Once a digital manifest of genome sequences has been constructed, different strains of the virus can be checked against each other for mutations.
“And by looking at those mutations, not just in our samples but in this database of a hundred thousand samples, we can start to build these connections. We can build at a very small scale, and think of an outbreak that might be occurring here in Fairbanks, and connect two clusters of cases that don’t seem to have any obvious epidemiological connection, but maybe they share the same viral sequence," said Drown.
The process of genome sequencing can expose underlying connections between strains of the virus that aren’t obvious in traditional contact tracing methods.
On Friday, this series will conclude as Dr. Drown discusses specific viral mutations, how the virus iterates on itself, and the future COVID as we develop vaccines.
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