How UK was able to detect new coronavirus variant so quickly

The emergence of a new variant in the UK was first announced by the government last week. A total of 1,108 cases associated with the mutated version had been detected, health secretary Matt Hancock told Parliament on 14 December. At the time, scientists warned it was “something to keep an eye on”.

Five days later, and following the emergence of new data presented to No 10, London and the surrounding regions have since been placed into tier 4 restrictions in a bid to arrest the alarming spread of the variant, which is thought to be 70 per cent more infectious than the original virus.

Despite mounting concern over what lies ahead, the UK has been praised for the speed at which it was able to detect, analyse and act against this variant – called VUI 202012/01 – with the World Health Organisation notably thanking British scientists for their efforts.

The Covid-19 Genomics UK (COG-UK) consortium has been central to this work. At the start of the pandemic, the government invested £20m into the establishment of the body with the goal of sequencing as many Sars-CoV-2 viral genomes as fast as possible.

This process allows scientists to unravel the tangled genetic fabric of the virus and understand how it is ordered. The more scientists are able to know about the wiring, structures and codes that make up Sars-CoV-2, the better placed they are to make informed decisions regarding treatments, vaccine development and infection control.

In the nine months that have passed, COG-UK has shown its value in decoding more than 150,000 different genome sequences of the virus – a “colossal achievement”, says professor Sharon Peacock, director of the consortium.

Few other countries have come close to matching the UK’s output. Professor Peacock says the country is responsible for “about half” the world’s genome sequencing data, meaning that “if you’re going to find anything [of interest], you’re going to find it here first”.

To put it into perspective: the Welsh branch of COG-UK had sequenced roughly 4,000 genomes of Sars-CoV-2 over the past seven days – more than the whole of France has managed throughout the pandemic, according to Tom Connor, a professor at Cardiff University’s School of Biosciences.

“We are sequencing in the UK at a disproportionate rate to other people which means that we have a much better surveillance system for catching this,” he says.

“We know the virus is going to mutate and evolve. We must expect it’s going to evolve to transmit better in the population, as that's what evolution does. We have the infrastructure in place to detect when that’s happening from a genomic perspective and ask searching questions as a result.”

He warned that similar variants could be “popping up around the world” but, due to a lack of localised sequencing, are flying under the radar of health authorities.

The surveillance findings of COG-UK and its 200 partners, which are passed on to the government and the UK’s public health bodies, have therefore played a vital role in facilitating the identification of new virus variants – which is where VUI 202012/01 comes into the picture.

“It makes sense that it was detected first in the UK because they have probably the world’s best surveillance program,” says Angela Rasmussen, a virologist at the Georgetown Center for Global Health Science and Security in the US.

VUI 202012/01 was first identified in October from a sample taken the month before, according to Public Health England (PHE).

Online lab records suggest the first detected case of the virus was picked up in the government's Lighthouse Lab in Milton Keynes on 20 September, while PHE said that the person who provided the swab was from Kent.

Prior to the second lockdown, health officials were aware that something wasn’t quite right in the southeast region because cases were rising much faster than elsewhere in the country – despite the introduction of the tiered restrictions. As the second wave took hold, authorities began to investigate.

“We first saw [the variant] in samples which originated in September, as part of a look-back process,” says Prof Connor. He adds that it’ll prove near impossible to fully establish whether this mutated version of the virus was “introduced from somewhere else or evolved locally”.

At the time the first sample was recorded, the UK was averaging just 3,700 positive tests per day. By the start of November, the average number of positive results had jumped to 23,000 per day. Later that month, the mutated version is thought to have caused roughly 28 per cent of cases in London and other parts of southeast England.

From there, it has continued to spread at a rapid rate. Figures show that in the week up to 9 December, 62 per cent of cases and 34 per cent of hospitalisations across the capital were linked to the new variant. Similar rises driven by VUI 202012/01 were reported in the surrounding regions.

Thankfully, scientists in the UK have benefited from a stroke of good fortune that has aided efforts to keep track of the variant’s growth throughout the four nations.

“One of the mutations in this variant, by coincidence, makes it possible to recognise it in some of the PCR tests that are used in community-based testing in the UK,” says Dr Jeffrey Barrett, lead Covid-19 statistical geneticist at the Wellcome Sanger Institute.

“That signal we can see much more immediately than the sequence-based data and that means we have a little more up-to-date data that is more comprehensive.”

Essentially, one of the 23 mutations associated with this variant causes the deletion of a certain gene in the virus’ spike protein, which is targeted by a variety of the polymerase chain reaction (PCR) tests used throughout the country.

Despite this diagnostics “blindspot”, the tests are still capable of detecting Sars-CoV-2, and the absence of the S gene – as it’s called – has actually provided authorities with a means of distinguishing between the different variants of coronavirus that are circulating within the population.

Professor Peacock said the “S-gene drop-out” was “very fortuitous” in providing a marker for those tracking the spread of VUI 202012/01.

Although the UK’s genomics network was well-placed to pick up this new variant, more analysis is needed to answer some of the questions that surround it.

The estimated transmissibility of this latest mutated version is based on government modelling and has not been confirmed in lab experiments, according to Muge Cevik, an infectious disease expert the University of St Andrews.

Testing is also under way to determine whether the Covid-19 vaccines in development will be able to induce an immune response against the variant – though current evidence suggests this will be the case, with scientists and government officials “confident” that the jabs won’t be affected.

In the meantime, COG-UK will continue to do what it does best: keep a close eye on the virus and watch it how it shifts and changes in the months to come. “That's why we were set up,” says Dr Peacock. “That will be useful technology going forward as this won’t be the last mutation we're concerned about. It's going to be an ongoing story.”