Last December, the UK shocked the world with the announcement of a new variant of the SARS-CoV-2 coronavirus that seemed to spread faster than the original virus. That discovery was made possible by the COVID-19 Genomics UK Consortium, which had been sequencing viral samples to monitor the evolution of the virus. COG-UK, as it is known, is led by , who spoke to 快猫短视频 about her research.
What were you working on before the pandemic kicked off?
I was working in Thailand in disease research until 2009. When I came back to the UK, it was clear to me that genome sequencing of bacteria and viruses was on the cusp of being accessible to scientists in general. So I invested in understanding sequencing and how to apply it. My first study was looking at how sequencing performed in an MRSA [superbug] outbreak on a paediatric intensive care unit.
At what point did you start thinking about sequencing the coronavirus?
I was having conversations about the need for sequencing in early March 2020. People knew the virus would change because that鈥檚 what happens. By about 15 March, 20 of us got together and said, how聽would we set up a national sequencing capability? And the answer was to throw a net over everybody who could do it and say, come and help us. So the public health agencies, Wellcome Sanger Institute and 16 sequencing hubs around the country did. We didn鈥檛 waste any time.
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Did everyone agree that sequencing was important?
Some people thought the virus wouldn鈥檛 change enough to make it useful. The virus changes quite slowly, there鈥檚 limited genetic diversity compared to some other pathogens. But we continued anyway. And when October 2020 came and [significant] variants started to emerge, that meant that we were in a very strong position compared to some countries that had to really scale up quite quickly.
And you are now handing routine sequencing over to the public health agencies?
Yes, that was always part of the plan. We will go back to being a research network. We鈥檝e only just scratched the surface of what the [coronavirus] genome information is telling us. We鈥檙e trying to link it to other data sets 鈥� for example, human genome data. And we鈥檙e developing online learning modules in SARS-CoV-2 sequencing. We鈥檙e hoping that that鈥檚 going to contribute something important to a wider global ability.
With sequencing equipment more accessible than ever, how important is global training?
It鈥檚 vital. It鈥檚 not possible to just open up an Oxford Nanopore MinION [a tiny, cheap sequencer], squirt something in and expect to聽get good-quality data. You need to know how to ensure that the data that you get out at the end is聽high quality. And you also need to learn how to interpret the data.
At one point, the UK was sequencing more samples than the rest of the world combined. Why was the country so far ahead?
The US has sequenced more than us now, but yes, we can be proud of聽that. We started early. The [UK] government supported us, we got funding, we had the expertise in the network and equipment on the ground already. We also had a聽relatively connected healthcare system. In other places, testing is聽more fragmented, it鈥檚 quite difficult to link it up together. And聽there was also a huge sense of聽cooperation between people. 快猫短视频s don鈥檛 generally want to share all their precious data before they鈥檝e even looked at it, but that鈥檚 exactly what happened here.
How worrying is it that in a lot of聽countries there is still very little sequencing going on?
I am worried about that. You won鈥檛聽know if new variants are emerging, you won鈥檛 be able to characterise them. Sequencing is an absolutely critical partner to vaccine roll-out and development.
We are in a situation now where one new variant after another emerges and starts to go global. Could this continue for some time?
Yes, I think it鈥檚 likely, but not entirely predictable when or where. Variants of concern emerge quite rarely, but when they do, can聽have a very significant effect. I聽think there鈥檚 going to be further evolution of the virus so that it鈥檚聽either more transmissible or [can evade immunity], or both.
That sounds like bad news. Is the vaccine going to be enough?
I remain optimistic. We can still vaccinate against all the variants that we have at the moment, and new vaccines can be developed quite quickly. Part of reducing the聽risk of new variants evolving is聽to聽drive down rates of infection because the virus can only mutate if it gets an opportunity to spread from one person to another and replicate. So global vaccination is聽the absolutely central answer to聽controlling variants.
So far, by the time we have established that variants of concern are more dangerous, they have already spread around the world. Can we do better?
I think there鈥檚 two questions there. One is: can you ever stop a variant in its tracks when you find it? I don鈥檛 know of any instance where a聽variant has emerged and we purposely eradicated it. Evolution is against you if something emerges that鈥檚 fitter than the previous variants. The second is: can you get quicker at聽reaching the level of evidence you need to pull the ripcord, if a variant is more transmissible for example. The thing that takes the time is not the sequencing, but looking to see whether something is transmitting more than something else, or if it causes more severe disease or not.
What things about the coronavirus do you think people need to know?
We will need to learn to live with the virus. The other thing is that when a new variant is described, often all the alarm bells start ringing. But at the time, you don鈥檛 really know enough to be able to say whether it鈥檚 important or not.
What鈥檚 this year been like for you personally?
It鈥檚 been a huge privilege to be able to contribute. I think COG-UK has been a brilliant success, and it鈥檚 a very large number of people that have made that happen. Like [it has been for] many other people, it鈥檚 been really rather exhausting.
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