Sharon Peacock: Catching changes in the COVID virus

Sharon Peacock explains how effective genome sequencing can be for helping health professionals better understand viruses, which became very important a few years ago...

Sharon - I would say that before the pandemic, one virus that is very important to sequence is HIV. People who are treated with what's called antiretroviral therapy, which suppresses the virus in the body, can develop resistance to the treatment. What you really need to do is sequence parts of the virus to see whether the treatment you're going to give is effective or not. You can't do that in a test tube. You need to be able to sequence it. So sequencing has actually been really important for HIV treatment.

Chris - So you prove all this, and that was looking like a huge success story, and then a pandemic comes. And this is when really you took the knowledge that you'd gained and kind of gave it the biggest dose of steroids it ever could because all of a sudden you're in charge of what became the COVID Genomics Consortium for the UK. The whole world was looking at that data. Why don't you just outline for us exactly, a) what you did, and b) what it produced?

Sharon - When the pandemic began, it was clear that we would need to start sequencing the virus to look for changes in its genome. Changes in the genome could, for example, relate to changes in how it behaves — changes in transmissibility or the way it interacts with our immune system, for example — which could affect vaccine efficacy and the way it causes disease in people. Would it cause a more severe disease, or a less severe one? I considered it very likely that we'd need to sequence the virus. So myself and Patrick Vallance, the Chief Scientific Adviser to the UK at the time, had discussions and agreed that I would set up a sequencing capability for the UK.

Chris - That was very early then. Was this literally at the beginning of the pandemic? You said, look, we've got a problem. This is one way we should be addressing it.

Sharon - Yes, absolutely. It was before we had barely any cases in the UK, but we needed to prepare. It wasn't going to be something we could get ready overnight. It was going to be a massive enterprise to set this up. So the point of sequencing the virus was really to detect if it mutated or changed its sequence, which could lead to changes in how it was transmitted from one person to another, the rate at which that happened, or how it interacted with our immune system. That would relate to vaccine efficacy or the severity of the disease people developed. We needed a countrywide view.

So we aimed to set up a sequencing capability across the United Kingdom. We pulled together the four public health agencies of the UK, 16 academic universities and the Wellcome Sanger Institute. We connected that like a network to 100 NHS testing labs, and as they developed, all of the Lighthouse Labs doing community testing. If there was a positive sample, we would obtain it, sequence the virus, and look at its genome to see how it was evolving.

Chris - And so when people were seeing reports of what variant is prominent at the moment, that was your data that was informing what's on this almost virological radar screen for the country, really.

Sharon - Exactly. We aimed to sequence around 10% of all known positive cases. We generated all of the data. We put all the genome data into a secure database that could be accessed by scientists. It could also be accessed by public health agencies, so they could monitor what was happening in their regions. We also, in an anonymous way, deposited all of those genomes into an international database. People could see what was happening in our country from a genome perspective. We had open-source information, which was very helpful, given that this was a global pandemic.

Chris - Britain was effectively then a sort of barometer for the evolution of the virus. Did other countries then either want to work with you, or did they set up an equivalent taking a lead from what you were doing, to add to that and turn it into a global radar screen?

Sharon - Yes. Other countries were thinking about this too. At one point, nearly half of the genomes deposited into the international database were generated in the UK. We were one of the first out of the starting blocks to generate this kind of information. Others were hot on our heels — for example, South Africa was very effective, as were the Netherlands and Denmark.
I think the great pity for me was that many countries didn't have the resources to sequence, so they weren't in a position to understand what was circulating. And it also meant that when a new variant emerged — and it could emerge anywhere — we wouldn’t detect it quickly. Alpha emerged in Kent, but other variants emerged elsewhere. To detect them, we needed a global effort, and that came quite late.

Chris - Those data all exist now, don’t they? So presumably there are people mining into that, delving into it to learn things, even though the pandemic is thankfully in the past. The way you did that stands there as an example of how it can be done. And it's an enormous resource for us to continue to learn from.

Sharon - Yes. What it showed for the first time was that sequencing could be done on a very large scale. That was unheard of. You could sequence millions of viral genomes and make sense of that in terms of the virus’s evolution and what it means for us as humans. That was a moment in time when sequencing pathogens really came onto most people's radar, and they realised the true power of doing it. There were other lessons too from how we set it up. One of them was to go into action without hesitation. People might have thought, “You're wasting your time setting that up now,” but you can't move fast enough in a pandemic. The speed and the confidence with which we said, “This will be important,” mattered. The worst outcome would have been ending up with a lot of valuable scientific data — which is no bad thing. But the best outcome was the one we had: we could track the emergence of variants and understand what that meant for humans.

Chris - Is this policy for a future pandemic or Disease X now? Will they be back on the phone to you? Is it written in, baked in, that when the next pandemic lands, they’ll call Sharon to do this again?

Sharon - It's not baked in that they would call me. The COG-UK Consortium was closed down after three years. It had 600 people, mostly volunteers. They were paid by their universities or employers, but volunteered for us. What I would say is that if another pandemic comes along, we absolutely need to be sequencing that virus or organism as soon as possible and doing the same. We have created a blueprint for how you can do this, but COG-UK as an entity is no longer in existence. Public health agencies will have the capability to do sequencing on a smaller scale, but we've learned invaluable lessons from that process.

Chris - Some would say, though, that if we wait for the next pandemic, we've waited too long. Shouldn't we be doing this anyway, right now?

Sharon - There is a lower amount of sequencing, but in virological peacetime, public health agencies have other priorities. They'll use sequencing for TB, outbreaks, foodborne outbreaks, and so on. So the capabilities are there. I’d just say that the scale is not there for a global pandemic — that would need to be scaled up quickly.

Chris - People really noticed though, didn’t they? When the consortium stopped, it was almost like that radar screen went dark. You heard reporters, health commentators, and other medics saying, “We don’t know what variants are out there now. We don’t know what will be going into the vaccine because we can't get that sense of the trend of what the virus is doing,” that we had when it was active. It really was incredibly meaningful and very useful.

Sharon - I can only agree.