First sign of Omicon spreading in Britain: Chart shows uptick in CASES with super-variant hallmarks

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The super-mutant Omicron variant appears to now be spreading domestically in England even though only a few dozen cases have officially been confirmed, a new chart suggests.

Official data shows that the proportion of positive Covid tests with a mutation synonymous with the highly-evolved strain is on the rise. Like Alpha, or the ‘Kent variant’, Omicron has a specific alteration which means it can be detected through PCR tests without the need for genomic sequencing.

The proportion of positive tests in England with this so-called S-gene dropout has risen from 0.1 per cent in the past week to 0.3 per cent, the equivalent of one in 330. Scientists said the increase in S-gene dropouts suggests there could be hundreds of Omicron cases that are flying under the radar currently.

While the variant is likely only making up a small number of cases in the UK — where 50,000 people on average are testing positive each day, most with Delta — it is feared the country could be on the brink of a fresh wave.   

It comes as public health officials in Gauteng, the epicentre of South Africa’s outbreak, estimate the province’s R rate has surged from less than one to 3.5 in just a month — suggesting that every 10 infected people are passing the virus onto 35 others.

The Omicron strain has triggered a meteoric rise in cases in South Africa, mostly concentrated in Gauteng, since the country that first alerted the world about the highly-evolved virus on November 24.

Nationally, cases there soared to 11,535 on Thursday marking a 370 per cent rise in a week, and up a third on around 8,500 yesterday. It has become the dominant strain in the country in little over a week since it was officially discovered, making up 75 per cent of sequenced samples.

A pre-print from a university in South Africa published yesterday found that the new strain is at least two-and-a-half times better at re-infecting people than all other variants, which may offer an explanation for why it is spreading so fast.

While Omicron’s infectiousness seems unquestionable, there is growing uncertainty about how well it can evade vaccines and how severe the illness it causes will be. The World Health Organization (WHO) today revealed zero deaths around the world have been caused by the new variant.

Public health experts in South Africa and the WHO have insisted cases are only mild and vaccines should still be highly effective against the strain, despite a lack of data. And doctors in Norway, where 60 people caught Omicron at a Christmas party, say all those infected have mild symptoms, such as headaches and sore throats.

But UK Health Security Agency (UKHSA) epidemiologist Meaghan Kall warned that data currently suggests Omicron may be ‘worse’ than Delta — although the picture is still emerging. She said she was ‘highly sceptical’ that the strain causes milder symptoms, saying infections may only appear less severe because people have immunity against other variants, unlike in the first wave.

Meanwhile, a major British study in booster vaccines found that both Moderna and Pfizer triple the level of T cells in double-jabbed people, which the scientists said made them confident boosters will give very high protection against Omicron.

And Tory Party chairman Oliver Dowden today insisted people should ‘keep calm and carry on’ with their Christmas plans and parties despite the emergence of the variant — but Britain’s pubs, hotels, restaurants and clubs already set to lose billions say ‘the damage is already done’ as the cancellations continue.

Scientists won’t know the full scale of Omicron’s infectiousness, vaccine evasiveness or lethality for another two or three weeks, when they can isolate the virus in a lab and study its biology and test it against the blood of previously-infected or vaccinated people.

Just 29 cases of Omicron have been confirmed in England, — three in Westminster and two in each of Barnet, Buckinhamshire, Camden, Lewisham and South Northamptonshire. There have been a further 13 cases in Scotland, divided between Lanarkshire and the Greater Glasgow and Clyde area.

Nine of Scotland’s cases were linked to a single event on November 20 — four days before South Africa alerted the world to Omicron in a move which prompted the world to shut itself of from the nation. The fact the cases were already in the UK suggests transmission within the community is already taking place. 

Laboratories determine whether Covid PCR tests are positive by looking out for certain parts of the virus, one of which is the spike protein on the outside of the cell.

On Omicron, the spike has mutated so much that the tests cannot detect it and only confirm whether other parts of the virus are present in a person’s nose and throat swab to tell if they are infected.

Around half of PCR tests in England are processed by laboratories that use a detection kit that looks for the spike protein and two other parts of the Covid cell.

In the five days leading up to November 28, the proportion of confirmed positive tests that didn’t detect the spike protein increased from 0.1 per cent to 0.3 per cent. 

These kits usually detect the three parts of the Covid cell, but still confirm someone is infected when they detect any part of the virus.

Failing to spot the spike protein — scientifically known as S-gene dropout or S-gene target failure (SGTF) — has happened before with the Beta varitant, which was first spotted in South Africa, because it also had mutations on the spike protein that tricked the tests into failing to spot it.

Scientists in South Africa, where Omicron has caused an unprecedented surge in cases in, were alerted to Omicron because they spotted the S-gene dropout.

The changes on the spike protein has caused alarm among experts and raised concerns the strain could escape vaccine protection and natural immunity from a previous infection.

But genomic sequencing of positive Covid samples — laboratory analysis that identifies a virus’s genetic make-up, allowing variants and mutations to be detected — remains the only full-proof way to confirm if a Covid infection was caused by Omicron.

Dr Davies tweeted that the increase in S-gene dropout from the usual level of 0.1 per cent to 0.3 percent between November 24 and 28 ‘represents about 60 more SGTF cases than we would expect to see.

‘Given that Omicron causes SGTF, while the otherwise globally dominant Delta variant doesn’t, these “excess” SGTFs are most likely Omicron cases, at least some of which have yet to be confirmed via sequencing.

‘However, this number will probably go up, as the last 2-3 days of data are still filtering in.

He tweeted: ‘The fact that there has been an increase in SGTF isn’t necessarily surprising — we have 22 confirmed Omicron cases in England as of today, so there was going to be an SGTF signal sooner or later. This isn’t meant to be shocking news.’

The apparent increase in Omicron cases could suggest the variant is being spread in the community, or signal that more international arrivals — who are required to take a PCR test within 48 hours of arriving in the UK — are testing positive.

Dr Davies added: ‘In a manner of speaking, we have been lucky in the UK that first Alpha had SGTF, then Delta didn’t, and now Omicron does.

‘Each time, we have been able to use the presence or absence of SGTF to detect probable VOC [variant of concern] cases a few days before the sequencing data has been available.

‘The SGTF signal also makes it easier to monitor the severity of a new variant, since it gives us another way to classify a case’s lineage and then to see whether a given lineage is more or less likely to lead to severe disease.’

And NERVTAG, a committee that advises the Government on the threat posed by new and emerging respiratory viruses, today said there are no other Covid variants in South Africa that cause S-gene dropout.

All of the S-gene dropout samples sequenced in South Africa went on to be confirmed Omicron cases, so it is ‘currently a reliable marker of the variant’. 

Meanwhile, it was revealed today that the R rate in Gauteng, the epicentre of South Africa’s outbreak, has soared from less than one to 3.5 in just a month — suggesting that every 10 infected people are passing the virus onto 35 others.  

It comes after data from the National Institute for Communicable Diseases (NICD) released yesterday evening showed 11,535 new Covid cases were recorded in the previous 24 hours, a jump of 368 per cent on last Thursday when 2,465 new infections were registered.

Some 51,402 people in the country took a Covid test and 22.4 per cent of them tested positive for the virus. For comparison, 38,075 per cent of tests taken on the same day last week and 6.5 per cent were positive.

Meanwhile, hospitalisations rose by 180 per cent in the last seven days. Some 98 people were admitted last Thursday, while 274 Covid-infected patients required hospital care yesterday.

But Covid deaths have decreased from 114 last Wednesday to 44 today, marking a 61 per cent fall. Trends in hospitalisations and deaths lag two to three weeks behind the pattern in cases, due to the time it takes to become seriously unwell after catching the virus.

And a preprint published by scientists from the Stellenbosch University, near Cape Town, suggests Omicron is at least 2.4 times more likely to reinfect someone than the original strain.

Government researchers say there has been 35,670 reinfections since the beginning of the pandemic and the risk of reinfection fell to 0.7 during the Beta-fuelled second wave last winter and the third Delta surge this summer compared to the first wave.

But the risk of catching the virus again has risen for the first time, jumping to 2.4.

Scientists from the Stellenbosch University, near Cape Town, said the findings suggest Omicron is able to evade protection people have from a previous infection, unlike the Beta and Delta variants that were suppressed by natural immunity.

They said the data has important public health implications, especially in countries that have previously had high rates of infection.

And ‘urgent questions remain’ over whether Omicron can evade vaccine protection just as well as natural immunity, and if so, whether this impacts hospitalisations and deaths.

Microbiologist at Reading University Dr Simon Clarke said the data was the ‘first indication’ that Omicron could get around immunity from previous Covid infection.

He said: ‘There are a few caveats in this work, such as not having definitively confirmed that it was indeed Omicron that was causing the reinfection, but they were able to determine that the increased transmission of Beta or Delta variants was not a result of immune evasion.

‘There is no indication as to how this immune evasion happens, although it can be presumed to be because of decreased antibody binding to Omicron’s mutated spike protein.’

He added: ‘Omicron has blown a big hole in the controversial argument that we should simply allow the infection to spread in an attempt to create immunity.

‘Herd immunity which now seems like nothing more than a pipe dream. We await a further indication as to whether Omicron has any ability to evade vaccine induced immunity.’

Scientists are working at breakneck speed to establish whether Omicron is more transmissible and deadly than other mutant strains. But they say it could still be at least a week before reliable estimates start to emerge.

Early reports on the ground in southern Africa suggested that most cases were mild or completely asymptomatic.

But there has been no age breakdown meaning it is impossible to know whether this is because the strain is simply yet to spread to older people.

The WHO has repeatedly claimed that it is a mild strain. Christian Lindmeier, a spokesperson for the global agency, today told reporters in Geneva: ‘I have not seen reports of Omicron-related deaths yet.

‘We’re collecting all the evidence and we will find much more evidence as we go along.

‘The more countries… keep testing people, and looking specifically into the Omicron variant, we will also find more cases, more information, and, hopefully not, but also possibly deaths.’

And doctors on the ground in Norway, where 60 people fell ill with suspected Omicron after attending a Christmas party last week, said those infected are currently experiencing mild symptoms.

Dr Tine Ravlo, chief physician for the district where the outbreak took place, said the patients are experiencing headaches and sore throats, broadly consistent with what is being reported from South Africa.

Only one of the cases has so-far been confirmed as Omicron using genetic sequencing techniques, with 10-15 cases declared probable Omicron.

But all cases are assumed to be the new variant, with the results of more sequencing tests expected soon.

Mr Ravlo said the ‘incubation period’ of the new variant — the time from infection to first symptoms — appears to be two to four days.

That is far less than the seven to 14 days for most other Covid variants, and would potentially make outbreaks easier to spot — though the data is still preliminary.

Mr Ravlo added that, so far, all infections in Oslo have been traced to the Christmas party and there is no evidence of wider community spread.

But Dr Kall said she is ‘sceptical’ about claims the new strain causes less severe disease.

Writing on Twitter, she said: ‘I am highly sceptical it could be more mild. I think the best case is it’s equivalent in severity to Delta… but you’ll see milder symptoms now, than Delta when it emerged, because many more people have immunity now.’

However, promising data from the UK’s COV-BOOST study suggests the body’s T-cell immune response after a third Covid injection will protect against hospitalisation and death from Omicron.

The findings also support the UK’s decision to use Pfizer or Moderna as boosters, with mRNA jabs turbocharging the body’s antibody and T-cell responses the most.

T-cells are thought to provide longer lasting and broader protection than antibodies which deliver an initial higher boost of protection but also see that defence fade faster over time.

Professor Saul Faust, trial lead and director of the NIHR Clinical Research Facility at University Hospital Southampton NHS Foundation Trust, said: ‘Even though we don’t properly understand its relation to long-term immunity, the T cell data is showing us that it does seem to be broader against all the variant strains.’

The provides ‘hope that a variant strain of the virus might be able to be handled, certainly for hospitalisation and death if not prevention of infection, by the current vaccines’, Professor Faust said.

It comes as Tory Party chairman Oliver Dowden today insisted people should ‘keep calm and carry on’ with their Christmas plans and parties despite Omicron – but Britain’s pubs, hotels, restaurants and clubs already set to lose billions say ‘the damage is already done’ as the cancellations continue.

Mr Dowden told Sky News: ‘The message to people, I think, is fairly straightforward – which is keep calm, carry on with your Christmas plans. We’ve put the necessary restrictions in place, but beyond that keep calm and carry on.

‘I understand that people have concerns around the new variant. That’s why the Government has taken the sort of measures that we’ve already outlined … we think those are sufficient at this stage and, beyond that, people should continue with their plans as intended.’

Amid confusion about what to do, many of Britain’s biggest employers including the NHS, banks and tech firms have axed festive bashes completely or taken them online. It is now said to be a 50/50 split.