Will It Sequence: Coronavirus
One of the questions we regularly ask on this podcast is: Will It Sequence? Can you take something like a dog, or a sample of fishtank water, and extract the DNA? Right now there’s a pandemic going on, but it’s worth asking: Will It Sequence? Can you gene sequence the coronavirus, and why would you want to? Phil Sansom asked Neil Ward from Illumina…
Neil - Yes, we can sequence the whole genome of coronavirus. Someone will have a swab taken of their nose or their throat and then we can extract from that the genetic code that makes up the virus. Now normally we sequence DNA. In the case of the coronavirus it's a slightly different type of code, it's called RNA.
Phil - So can you read RNA the same as DNA?
Neil - We convert that actually into DNA. Once we've converted it into DNA we can put it onto our sequencing machines, and then we can read the As, Cs, Ts, and Gs, and understand that sequence.
Phil - How hard is that? How big is this amount of RNA that you've got to read?
Neil - Well fortunately for the world in this case, the RNA genomes are much smaller than the human genome. So human genomes are three billion letters long. That's a big book of instructions. Whereas the virus is actually really pretty tiny, it's thirty thousand letters.
Phil - If human DNA is like the complete works of Tolkien, what is the virus RNA in comparison?
Neil - I don't know, it's like 'Spot the Dog'. Not sure if that's one that's familiar with the audience there? But it really is very simple, a small number of words that we can quickly read through and get an understanding of the full story of the genome of that virus.
Phil - What story are you talking about here? What can you understand?
Neil - Well there's a lot we can do from looking at that viral genome, and the diagnostics that are being used today around the world testing hundreds of thousands of individuals to see whether they have the disease are a really simple genetic test, they're called an RT-PCR test.
Phil - RT-PCR?
Neil - Yeah. Reverse transcription, so that's the first step of converting the RNA into DNA; and then PCR, a polymerase chain reaction, which is a process that we do to make copies of the DNA, to amplify the amount of material such that it becomes measurable on simple machinery.
Phil - Apart from just looking for the virus itself, there's other uses for genetics here aren't there.
Neil - Yeah, what many people are trying to do with the coronavirus genome sequencing at the moment is build a family tree. And that ability to do what's called genomic epidemiology has been game-changing in the last five to ten years. Historically, if you went back prior to the use of whole genome sequencing, the public health bodies when they found multiple individuals that seemed to have the same disease would go through a series of questionnaires asking them where they've been the day before, or where they've been that week; and I don't know about you, I struggle to remember what I was doing this morning, let alone last week and who I've met. So that type of information was really difficult to get to the underlying causes and who had infected who. The sequence information that we have here is nowadays layered onto that type of questionnaire, and increasingly other electronic information as well. And collectively that allows people to build a much better understanding of how the virus is spreading.
Phil - Now obviously things aren't too good for the world right now. I'm recording this from lockdown. I think I'm right that you're in lockdown over there yourself?
Neil - Indeed. It's a challenging time. My kids have not yet interrupted, but many of us are working from home with family members. It's changing life significantly. And you're right, for many people they're concerned, they're worried, and hopefully the genomic data will go on to allow pharmaceutical, biotech, and other researchers to better understand the viral genome, with the long term aim of being able to design some vaccines or being able to design new antiviral therapies so that we can get out of this situation of having the world locked down.