‘Secret weapon’: vaccine not the only thing Britain got right

At first considered pointless, Operation Eagle is giving Britain the edge in the cat and mouse war with virus evolution.

Swab kits are being delivered to 80,000 people as part of Operation Eagle, a surge testing programme.

Global medical revolutions rarely arrive with a knock on a Maidstone front door, but this week, with all the banality of an Amazon delivery, that’s exactly what has been happening.

In eight postcodes in the southeast, the northwest and the West Midlands of England, home swab kits are being delivered to 80,000 people as part of Operation Eagle, a surge testing programme.

Its goal is to rapidly identify and isolate people infected with the South African variant of coronavirus. In doing so, though, it is reinforcing a global view that it is not just the vaccine procurement that Britain got right.

This is a programme that at first many thought pointless but which has in past months risen in prominence. The UK is, as TheWallStreet Journal put it this week, the “world leader in sequencing the coronavirus genome”.

Eventually, some of those Maidstone swab kits will find their way to one of the most famous genetics laboratories in the world: the Sanger, named in honour of Fred Sanger, who won the Nobel prize (his second) for work on decoding DNA. Twenty years ago this laboratory used that technology to help fully sequence the first human genome. That took years of work and hundreds of millions of pounds.

This week though, the Sanger, in Hinxton, near Cambridge, will sequence more than 10,000 genomes - not of humans, but coronaviruses. These Maidstone test kits are part of what many scientists believe is a significant advance - another public health tool, to add to antibiotics, vaccines and sanitation.

The pandemic has brought forward many revolutions - remote working, vaccine technology, video conferencing. Sequencing is another. For the first time we are using genetics at a large scale to track and combat the evolution of a virus.

But it begins with delivery. When the kits arrive, people are asked to take out a testing kit and swab the back of their throat. When the samples arrive in the testing laboratory, they will be one of thousands entering a production line of PCR tests, but they will also be different. They will be flagged “Operation Eagle” and if they are positive then, unlike the other samples, this is not where they will stop. We need to know what they are positive with. Their sample has another journey ahead of it.

A mutation is tiny, a few changes in just a few atoms, but it comes with momentous economic, social and healthcare consequences. The first time the E484K mutation was discovered at scale was in South Africa. Looking at the changes it wrought to the viral structure, scientists feared it could help it evade immunity. Looking at the findings from vaccine trials, they had their confirmation.

This is what the surge testers are looking for. While Dido Harding, the head of the UK’s test and trace programme, has been building the infrastructure, what has been largely missed is that behind it a second one has been developed.

Last March, right at the start of the pandemic, a group of geneticists got together to see what they could contribute.

Their plan was to do something that has never been done before - produce the full genome sequence of the virus in as many infections as they could. Their presumption was that by looking at the mutations, they could provide useful information to stop the pandemic.

“People were saying what a waste of time [and] money,” says Sharon Peacock, the Cambridge geneticist who runs the Covid-19 UK Genetics Consortium (Cog-UK).

Their critics were wrong. Without Cog’s work, it is unlikely that the Kent variant would have been spotted so quickly or that there would have been hope of running surveillance on the South African one.

When this Maidstone sample tests positive, it is put aside, ready for the daily courier. Each day, throughout the pandemic, between 5 and 10 per cent of all samples don’t end their life at the testing laboratory. Instead in their hundreds of thousands, in an effort that dwarfs that of any other country, they have gone to a second laboratory.

For most, that second laboratory is the Sanger.

It was not designed for its present role. “Everything had to be set up from scratch,” says Catherine Ludden, Cog’s director of operations. “It requires huge teams. You’ve got people working round the clock who volunteered to give up the last year of their lives.”

Even as testing laboratories were being built from scratch, this team needed to co-ordinate data protocols, barcode identifiers, the boxes they used, the plates the samples came from. They needed to ensure that not only could they identify the samples, but so could the robotic arms that pipetted them out into the sequencer - the device that takes the Maidstone sample and finds out just how worrying it is. Reading genetic material has not been performed in a production line like this before.

A day after it arrives, the Operation Eagle sample will join those of every other genome sequenced here. Anonymised and placed on a global database in which almost half the entries are from the UK, it is ready to be used by the scientific community.

If, however, it contains the tweaks associated with the South African variant a non-anonymised version is sent to the public health teams in Maidstone, giving them the information to track, and hopefully stop, its spread.

Alan McNally, professor in microbial genomics at the University of Birmingham, has been working to set up lighthouse labs since the pandemic began. He is expecting his first Operation Eagle samples soon.

“We’ve been fighting to use this as a tool for ten years in infectious diseases,” he says. “One of the lasting legacies for public health in this country after Covid will be that we know the enormous power of doing real-time genomic surveillance of infectious diseases.”

To fight the virus we have the vaccine. To fight the vaccine, the virus has mutations. Now, in this cat and mouse war with evolution, to fight the mutations we have genomics.

The Times