Finding mutant coronaviruses

Across the UK, coronavirus cases are now thankfully falling. But the surge in coronavirus cases we’ve been suffering was triggered in the first place largely by the combined effects of winter, which helps viruses to spread more efficiently, and a more transmissible "new variant" of the virus thought to have emerged first in the southeast of the country and which may, according to UK Chief Scientist Patrick Vallance speaking at a recent Downing Street Press Conference, also carry a slightly higher mortality rate than the parent virus.

Katie - Other countries have also detected mutant coronaviruses that have enhanced abilities to transmit, and possibly sidestep our vaccines. This has prompted the government to put in place measures to block travellers entering the UK without a prior negative test. Transport secretary Grant Shapps outlined these measures recently...                                                                                                                                                                                                                                   

Grant Shapps - What we're trying to do now is stop a new variant, which isn't established here, from coming here. So we've done this today and I notice the Canadians - the prime minister Justin Trudeau there - has done exactly the same thing as us. Also introducing a 72 hour test in addition to the quarantine measures which remain in place.

Adam - But one of the reasons why we know about the new UK variant, and found out so quickly, is thanks to a consortium called COVID-19 Genomics UK, or COG-UK. It's led by Sharon Peacock from the Dept of Medicine at Cambridge University. She told Chris Smith how the initiative works, and, interestingly, speculated that one reason why covid is surging in so many countries is that variants like those we've picked up here might be a lot more common around the world than we think…

Sharon - COG-UK is a network of around 300 people who are scattered all around the country, to sequence the cause of COVID-19, the virus SARS COV-2 virus, to track important changes in the virus, as it evolves. So far in our efforts, we've sequenced around 200,000 genomes in total. Now to try and contextualize that, we have contributed around just under half of all the global genomes that are available for this virus at the moment.

Chris - And when you sequence the genome, what's actually involved in that and how do you get access to those samples in the first place?

Sharon - Well, we get samples after people have been tested and so, the diagnostic test, this is the PCR assay. We take the waste from that has been extracted from the sample for that test and we use it to prepare some further material that can be sequenced in a sequencing machine. The end result is that we have the genetic information for that virus, which is around 30,000 different points in the genome.

Chris - So 30,000 genetic letters long, it's quite big, what do you then do with that information? Because you basically have ended up with a giant document, which is 30,000 letters long. What do you do next?

Sharon - We're interested in two particularly important things. Has the virus developed a mutation - that means a mistake or a combination mistakes, actually more often a constellation of mistakes - that could change the way that the virus actually behaves and interacts with humans. The other way is that we compare the entire genetic code with that of other viruses and we can use that to look at issues such as has there been an outbreak.

Chris - So when you've read the genetic code for a sample and maybe you could tell us also how you choose where around the country you sample, or is it just random? Do you then basically line up your new sequence you've got from that sample with the sequences that you've read before and ask, is this one, any different?

Sharon - There were two parts to your question. The first is where do we get the samples from and how do we choose them? We try to cover the entire country. We aim to get samples from people who have infection and who are in the community and don't need to go into hospital. We also obtain viruses from people who have been admitted to hospital because you want the entire spectrum. And then when we have a full genome of a virus, we will compare it to other viruses, bit like a family tree. We also have software tools that really help us identify particular points in the genome that are of concern to us because for example, they could be related to a greater transmissibility spread between people or possibly the way they interact with the immune system.

Chris - And when the new variant that a lot was made of this around Christmas time but in fact, it began to emerge much earlier than that didn't it? How did you first notice that and how did you then track it? How did you realise it was significant?

Sharon - It was only looking backwards that we realised the very first sequence was sequenced on the 20th of September last year. And it's actually looking for new variants is like looking for a needle in a haystack because there are thousands and thousands of new mutations in the virus. And so looking for one that's important can be very challenging. It was only really in mid to late November when it really became clear that there seemed to be a spread of cases in the South of England. Whereas there wasn't spread in other parts of the country that were under similar lockdown rules. There are a range of explanations for that, but one of them is the virus could be somewhat different in its behaviour. So at that point, people that have information on populations and clusters of cases realised that the two could be related. It seemed to be an increasingly transmissible virus linked to a very specific genome.

Chris - And do you think this is going on in terms of making these sorts of very transmissible viruses all over the world? And it's only because we have you that we know about it, or are we a special case?

Sharon - I don't think we're a special case at all. The force of nature is being seen across the world, but you're only going to see what you seek. And so we, because we are sequencing around half of the world's genomes, are likely to detect those mutations. But the similar mutations that are going to be important in terms of transmissibility and vaccination are very likely to emerge from around the world. And in fact, we're seeing that sort of pattern happening now.