How Britain shot itself in the foot being the ‘best in the world’ at sequencing viruses

The UK is being punished for a mutant strain of coronavirus, which scientists say could have emerged elsewhere and was only spotted thanks to Britain’s world-leading genetic sequencing capabilities.

Britain sounded the alarm about VUI-202012/01 over the weekend after an explosion of cases in the South East of England and London were linked to the strain, which was first detected in a patient in Kent in September.

The UK was then made an international pariah as countries shut their borders to UK travellers in a bid to contain the spread of the variant, thought to be 70 per cent more infectious than regular Covid.  

Yet if it wasn’t for the Covid-19 Genomics UK (COG-UK) consortium, hailed as the ‘best genomic sequencing programme in the world’, it would have likely slipped under the radar and proliferated global infection rates.

Top virologists in the US admitted today the strain could have emerged there and went undetected because America’s genomics scheme is ‘sporadic’, while Covid variants with near-identical genetic make up have been reported in South Africa and Brazil.

Belgian’s top Covid expert said the ‘variant has already spread more than we think’, and claimed it was not ‘completely fair’ to slap travel bans on the UK simply because its advanced genome sequencing had detected the mutation first. 

Outside the UK, cases of the new strain have already been identified in Denmark, Gibraltar, the Netherlands, Australia and Italy. Germany’s health institute said today it was highly likely that the mutation was already in the country, although it had not been detected yet. 

The COG-UK consortium is on its own responsible for generating and making publicly available more than 100,000 genomes of the disease, accounting for 50 per cent of the contributions from the rest of the world combined.

Its work on Covid genomes — the virus’ genetic information — have helped scientists understand and track the virus as it evolves, allowing vaccines and life-saving treatments to be developed at unprecedented speed.  

COG-UK is the most joined-up consortium of its kind worldwide, bringing together the NHS, the four public health agencies across the UK, 13 leading universities and the Wellcome Sanger Institute, one of the largest genetic and genomic sequencing centres in the world.

 

 

The partnership was established in early March as it began to become clear the world was facing its most serious viral outbreak in modern history. It has been backed by £32.2million of funding from the Department of Health and Social Care. 

Samples from patients with Covid-19 are collected by NHS laboratories, public health laboratories and national coronavirus ‘Lighthouse Lab’ testing centres as part of their routine diagnostic work.

Genome sequencing is then performed by a network of regional laboratories which includes Belfast, Birmingham, Cambridge, Cardiff, Edinburgh, Exeter, Glasgow, Liverpool, London, Norwich, Nottingham, Oxford and Sheffield, backed up by a national sequencing hub at the Sanger Institute.  

Online records show the first case of the mutated strain spreading rapidly through England was identified in mid-October at Public Health England’s laboratory in Milton Keynes. It was found in a sample provided on September 20 in Kent.

News about its existence would then have been sent to the Covid-19 Genomics Initiative at the Wellcome Sanger Institute, led by Dr Jeff Barrett.

Dr Barrett’s team is developing tools and techniques to provide real-time genomic monitoring of SARS-CoV-2 in the UK to aid public health response. The team is constantly monitoring genetic mutations which could cause the virus to be more easily transmitted or to escape vaccines.

Some of the faces behind COG-UK: Researchers at the Wellcome Sanger Institute, one of the largest genetic and genomic sequencing centres in the world, who have been generating Covid genomic sequences

Some of the faces behind COG-UK: Researchers at the Wellcome Sanger Institute, one of the largest genetic and genomic sequencing centres in the world, who have been generating Covid genomic sequences

Where are COG-UK's labs? Genome sequencing is performed by a network of regional labs which includes Belfast, Birmingham, Cambridge, Cardiff, Edinburgh, Exeter, Glasgow, Liverpool, London, Norwich, Nottingham, Oxford and Sheffield, backed up by a national sequencing hub at the Sanger Institute

Where are COG-UK’s labs? Genome sequencing is performed by a network of regional labs which includes Belfast, Birmingham, Cambridge, Cardiff, Edinburgh, Exeter, Glasgow, Liverpool, London, Norwich, Nottingham, Oxford and Sheffield, backed up by a national sequencing hub at the Sanger Institute

Tracking of samples of the new variant by COG-UK shows that cases have been found all over England, as well as in south and north Wales, and in Scotland. The green dots are not relative to the number of people infected and may only represent one person. Experts said 'by far the highest concentration' of cases is in London, the East and South East of England

Tracking of samples of the new variant by COG-UK shows that cases have been found all over England, as well as in south and north Wales, and in Scotland. The green dots are not relative to the number of people infected and may only represent one person. Experts said ‘by far the highest concentration’ of cases is in London, the East and South East of England

When it became clear the new strain was quickly becoming the predominant strain in London and the South East earlier this month, the COG-UK team alerted NERVTAG, an expert committee advising the Government on Covid. 

The decision was then made on Saturday that those regions needed to be upgraded to a draconian Tier 4, crushing Christmas plans for 16millions Brits.

Scott Gottlieb, a former head of the FDA, told CNBC that the new strain ‘is already in the US’ and that a travel ban would not keep it out. ‘As the virus continues to spread around the world, we’re going to start to see more of these variants,’ he warned. 

Jeremy Luban, a University of Massachusetts virologist, told the Washington Post that the new strain ‘may have even started here’ – suggesting it might have been detected in Britain first because the UK has a genome sequencing program hailed as the ‘best in the world’ compared to the ‘sporadic’ one in the US. 

‘It may very well be here. It may have even started here. The sequencing in the US is so sporadic,’ he said. 

New York governor Andrew Cuomo also said he believed the new strain had reached the US, while Dr Anthony Fauci said that ‘you really need to assume it’s here already’. 

‘I would not be surprised at all if it’s already here,’ Fauci told Good Morning America – saying that compulsory testing might be needed to fly to the US but that banning travel completely would be a ‘rather dramatic step’. 

Dr Shira Doron, an epidemiologist in Boston, told NBC10 that she ‘can’t imagine it wouldn’t be’ in the United States already. ‘Would I expect to see that variance in the US? Of course. People are traveling all the time. I would expect to see that,’ she said. 

Angela Rasmussen, a virologist at the Georgetown Center for Global Health Science and Security, said it would ‘not shock me at all to find out’ that the strain is already in the US. 

‘I don’t think a travel ban is going to be particularly helpful. We already have out-of-control transmission of all the variants that are circulating in the US here,’ she said. ‘It makes sense that it was detected first in the UK because they have probably the world’s best surveillance program.’

A scientist on the UK’s advisory panel, Calum Semple, warned on Monday that the new mutation was likely to become the dominant strain around the world – predicting that it would ‘out-compete’ other forms of the virus.  

How the mutated form of Covid has rapidly spread across swathes of England over the last fortnight 

The mutated coronavirus strain has rapidly spread through swathes of England in a fortnight, according to official data that shows it now accounts for the majority of infections in some regions.

The Office for National Statistics estimates 62 per cent of cases in London were because of the new variant in the week up to December 9, the most recent snapshot provided by the Government agency. That was almost double the amount of infections in the capital attributed to the mutation in the seven-day period to November 25 (35 per cent).

It’s believed the new variant — thought to be up to 70 per cent more infectious than regular Covid — emerged in a patient in Kent and made its way into London and the commuter belt.

In the East of England, the strain is estimated to have made up 59 per cent of infections in the week to December 9, soaring from 31 per cent the two weeks prior. The ONS said 43 per cent of cases in the South East in the most recent week were cause by the variant, up slightly from the 39 per cent on November 25. 

Smaller rises were seen elsewhere in the country. In the Midlands the figure jumped from 19 to 27 per cent, in the South West the figure rose from 27 to 28 per cent and for the North West it went from 12 to 17 per cent.

The North East and Yorkshire actually saw declines in cases of the super-charged strain, with the percentage of cases falling from 18 to 15 per cent and seven to five per cent, respectively. 

The data comes from the ONS’ Infection Survey, which has been monitoring Britain’s crisis by sending tens of thousands of swabs to random households across the country, regardless of whether people have symptoms.

As the new strain becomes more widespread and triggers a third wave of infections, there are fears that hospitals could become overwhelmed and deaths could approach the devastating levels seen in spring.

But scientists have assured the public there is no evidence to suggest it is more lethal than regular Covid and have even suggested it could be less dangerous. From an evolutionary standpoint, viruses can transmit more easily if they cause mild or asymptomatic illness because it means carriers continue to go about their daily lives, thereby spreading the contagion more extensively.

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The mutation has been blamed by UK politicians for a resurgence in cases in the south of England which seemed to defy a November lockdown. But other experts have played down concerns, saying the 70 per cent claim is unproven. 

At a briefing on Monday, UK scientists said the potential vulnerability of children ‘might explain a significant proportion’ of the overall rise in cases. In England’s most recent national lockdown, schools stayed open while shops, bars and restaurants all closed. 

The coronavirus has long been seen as ‘not as efficient in infecting children as it was in adults’. But scientists believe the new strain may have changed this.    

‘There is a hint that it has a higher propensity to infect children,’ said Neil Ferguson, an epidemiologist at University College London and member of an advisory panel. 

‘We haven’t established any sort of causality on that, but we can see it in the data,’ Ferguson said. ‘We will need to gather more data to see how it behaves going forward.’ 

He added: ‘What we’ve seen is, during the lockdown in England we saw a general distribution of the virus towards children, and that was true in the variant and the non-variant, and it is what we would expect, given that we had locked down which reduced adult contact but schools were still open. 

‘But what we’ve seen over the course of a five or six-week period is consistently the proportion of [cases] for the variant in under-15s was statistically significantly higher than the non-variant virus. We are still investigating the significance of that.’  

Another UK scientist, Professor Wendy Barclay of Imperial College London, said the new virus might ‘put children on a more level playing field’ compared to adults. 

The UK government believes the new variant may explain why cases kept rising in parts of England even during the November lockdown.

Since the lockdown ended, cases have risen again across the country – leading to tough new restrictions and this week’s rush to shut down flights.   

Belgian virologist Marc van Ranst warned that ‘this variant has already spread more than we think’, telling Bloomberg that it was not ‘completely fair’ to slap travel bans on the UK simply because its advanced genome sequencing had detected the mutation first. 

Cuomo said on Monday that the new strain was ‘another disaster waiting to happen’ after New York was hit hard by the first wave of the pandemic in the spring.

‘When you do not require flights from the UK to be tested, you are allowing thousands of UK passengers to arrive here every day,’ Cuomo said. ‘Based on New York’s experience in the spring, I believe this new, highly contagious strain of Covid-19 is already here,’ he added. 

Virgin Atlantic, British Airways and Delta Airlines have already agreed to test all passengers for Covid-19 prior to boarding UK flights for New York. 

The White House coronavirus task force is also considering a new rule that would require all passengers arriving from the UK to have a negative test within 72 hours of departure.  

Canada has already imposed a 72-hour ban on arrivals from the UK, making it one of more than 40 countries to have shut down travel from Britain.  

Outside the UK, cases of the new strain have already been identified in Denmark, Gibraltar, the Netherlands, Australia and Italy. 

Germany’s RKI health institute said today it was highly likely that the mutation was already in the country, although it had not been detected yet. 

France, which closed its border to lorries on Sunday as well as cars and passenger transport, said there was no evidence so far that the strain was circulating there. 

QUESTIONS ANSWERED ON NEW COVID MUTATION: HOW DID IT HAPPEN, IS IT MORE DANGEROUS AND HOW LONG HAS IT BEEN IN THE UK?

By David Churchill

What has happened to the coronavirus to trigger such concern?

A new strain of Covid has developed which is said to spread far faster. A ‘strain’ is a new version of a virus which has genetic mutations. The new strain is a version of Sars-Cov-2, the coronavirus which causes the disease Covid-19.

It has been named VUI-202012/01. These letters and numbers stand for ‘variant under investigation’ and the month, December 2020.

What makes it so worrying?

This particular variant is defined by up to 17 changes or mutations in the coronavirus spike protein. It is the combination of some of these changes which scientists believe could make it more infectious.

It is thought they could help the virus’ spike protein latch on to human cells and gain entry more easily.

Is it certain the new variation is accelerating the spread of the virus?

No, but scientists say preliminary evidence suggests it does.

Boris Johnson said it may spread up to 70 per cent more easily than other strains of the virus, potentially driving up the ‘R rate’ – which measures how quickly the virus spreads – significantly.

On Saturday night, Mr Johnson said it could drive up the ‘R rate’ by as much as 0.4.

This would be particularly significant in areas such as Eastern England, where it is 1.4, and both London and the South East, where it is 1.3. The ‘R rate’ must remain below 1 for infections to decrease.

Is the new variant more dangerous?

Scientists don’t think so for now. When asked on Saturday night if it was more lethal than the previous strain, Chief Medical Officer Professor Chris Whitty said ‘the answer seems to be ‘No’, as far as we can tell at the moment’.

Yesterday Dr Susan Hopkins, of Public Health England, said there was evidence of people with the new variant having higher viral loads inside them.

But she said this did not mean people would get more ill.

Ravi Gupta, professor of clinical microbiology at the University of Cambridge, said: ‘It’s unlikely it’ll make people sicker, but it could make it harder to control.’

If it does make the virus harder to control and hospitals become overrun, it could pose new challenges.

Are mutations unusual?

No. Seasonal influenza mutates every year. Variants of Sars-Cov-2 have also been observed in other countries, such as Spain.

However, one scientific paper suggests the number and combination of changes which have occurred in this new variant is potentially ‘unprecedented’.

Most mutations observed to date are thought to have happened more slowly. Also, most changes have no effect on how easily the virus spreads.

There are already about 4,000 mutations in the spike protein gene.

What has caused the mutation?

This is still being investigated. One theory is that growing natural immunity in the UK population, which makes it harder for the virus to spread, might have forced it to adapt.

Another theory is that it has developed in chronically ill patients who have fought the virus off over a long period of time, with it then being passed onto others.

Prof Paul Hunter, Professor in Medicine at the University of East Anglia, yesterday said it was ‘plausible’ and ‘highly likely’ this has happened.

However, he stressed it is impossible to prove at the moment.

What evidence is there to support the latter theory?

Some evidence supporting it was spotted when samples of virus were collected from a Cambridge patient. They had been treated with convalescent plasma – blood plasma containing antibodies from a recovered patient.

It is possible the virus mutated during that treatment, developing more resistance to the antibodies. This patient died of the infection, but it’s also possible the mutation has occurred elsewhere.

A paper co-authored by Andrew Rambaut, Professor of Molecular Evolution at the University of Edinburgh, states: ‘If antibody therapy is administered after many weeks of chronic infection, the virus population may be unusually large and genetically diverse…creating suitable circumstances for the rapid fixation of multiple virus genetic changes.’

Professor Hunter added: ‘Mutation in viruses are a random event and the longer someone is infected the more likely a random event is to occur.’

What do these mutations do?

Many occur in what’s called the ‘receptor binding domain’ of the virus’ spike protein. This helps the virus latch on to human cells and gain entry. The mutations make it easier for the virus to bind to human cells’ ACE2 receptors.

It is also possible the changes help the virus avoid human antibodies which would otherwise help fight off infection.

Who detected it?

It was discovered by the Covid-19 Genomics UK (COG-UK) consortium, which carries out random genetic sequencing of positive covid-19 samples.

It is a consortium of the UK’s four public health agencies, Wellcome Sanger Institute and 12 academic institutions.

How long has it been in the UK and where did it start?

As of mid-December, there were more than 1,000 cases in nearly 60 different local authorities, although the true number will be higher.

They have predominantly been found in the south east of England, in Kent and London. It may now account for 60 per cent of the capital’s cases.

But it has been detected elsewhere, including in Wales and Scotland.

The two earliest samples were collected on September 20 in Kent and another the next day in London.

Why was action to tackle it not taken sooner?

Because the potentially greater transmissibility was only discovered late last week by academics.

Has it been detected anywhere else in the world?

One aspect of the new variant, known as a N501Y mutation, was circulating in Australia between June and July, in America in July and in Brazil as far back as April, according to scientists.

It is therefore unclear what role, if any, travellers carrying the virus may have had.

Dr Julian Tang, a Virologist and expert in Respiratory science at the University of Leicester, said: ‘Whether or not these viruses were brought to the UK and Europe later by travellers or arose spontaneously in multiple locations around the world – in response to human host immune selection pressures – requires further investigation.’

Another change, known as the D614G variant, has previously been detected in western Europe and North America. But it is possible that the new variant evolved in the UK.

What can I do to avoid getting the new variant?

The same as always – keeping your distance from people, washing your hands regularly, wearing a mask and abiding by the tier restrictions in your area.

Yesterday Dr Chaand Nagpaul, chair of the British Medical Association, said: ‘The way in which you control the spread of the virus, including this new variant, is exactly the same. It is about continuing stringent measures. The same rules apply.’

Will the new variant reduce the effectiveness of vaccines?

More studies are needed.

Dr Susan Hopkins, of Public Health England, said that until these are carried out scientists cannot be certain whether – and by how much – the new variant reduces the effectiveness of developed vaccines.

She said: ‘The vaccine induces a strong, multiple response, immune response and therefore it is unlikely that this vaccine response is going to be completely gone.’ When mutations happen it is, in theory, possible the antibodies generated by vaccines can be evaded.

But vaccines produce a wide range of antibodies that simultaneously attack the virus from different angles, making it hard for it to evade all of them at once.

Vaccines could also be tweaked to make them more effective if the new mutation does prove to be more resistant to them.

So what are the scientists doing now?

Scientists will be growing the new strain in the lab to see how it responds. This includes looking at whether it produces the same antibody response, how it reacts to the vaccine, and modelling the new strain.

It could take up to two weeks for this process to be complete. 

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