New charts suggest that Omicron, the super-mutant Omicron strain is spreading within England even though just a few dozen confirmed cases are available.
Official data indicates that there is an increase in the percentage of positive Covid test results for the mutation associated with the extremely-evolved strain. Omicron, like Alpha or the ‘Kent variation’, has a particular alteration that can be detected by PCR without the need to perform genomic sequencing.
England’s proportion of S-gene-dropout positive tests has increased from 0.1% in the week prior to 0.3% in the current week. This is equivalent to one in 325. Scientists believe that there may be many Omicron cases still undiscovered.
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.
Since November 24, when South Africa was the first to alert the rest of the world, the Omicron virus has caused a rapid rise in Omicron cases. Most are concentrated in Gauteng.
The national rate of cases rose by 37% to 11,535 last Thursday. This is a significant increase from the 8,500 reported yesterday. Within a matter of weeks, the strain has become the most dominant in the country. It is responsible for 75% of the sequenced samples.
Yesterday’s preprint published by a South African university found that this new strain has a rate of at least two and a half times more success in re-infecting individuals than any other varieties. This may explain why it is so rapidly spreading.
Omicron’s infectiousness is undisputed, but there are growing concerns about its ability to evade vaccinations and the severity of the disease it will cause. Today, the World Health Organization revealed that the Omicron variant caused zero deaths in all parts of the globe.
South African and WHO public health officials insist that cases of Omicron are mild. Vaccines against this strain should be effective despite the lack of data. Doctors in Norway have confirmed that Omicron was infected in 60 cases at a Christmas party.
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. Although she is skeptical that Omicron causes milder symptoms than Delta, Kall said infections might only seem less severe if people are immune to other variants.
It was discovered that booster vaccines have been proven to be very effective against Omicron in a large British study.
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.
Omicron will remain unknown to scientists for at least two weeks. Scientists can then isolate the virus and examine its biology, and compare it with the blood of previously infected people.
Official data indicates that there is an increase in the percentage of positive Covid test results for the mutation associated with the extremely-evolved strain. Omicron is similar to Alpha and the ‘Kent varietal’. It has a unique alteration that allows it to be detected using PCR tests, without the need of genomic sequencing. England’s proportion of S-gene-dropout positives has increased from 0.1% to 0.3 percent in the week just before, the equivalent of 1 in 330. Scientists believe that there may be many Omicron cases flying unnoticed at the moment, as evidenced by the rise in S-gene dropsouts.
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. A further 13 Omicron cases were confirmed in Scotland. These are split between Lanarkshire, the Greater Glasgow-Clyde region and Scotland. 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. It is possible that transmission has already begun within the community by the fact that the cases are already present in the UK.
According to official data, nearly 900,000.00 people in England received Covid during any one week last week. The chart below shows the overall Covid rate.
South Africa’s data show that Omicron has taken control in Gauteng, and the R rate has shot up to above three percent.
According to experts who conducted a Government-funded study, booster vaccines for Covid may offer protection against Omicron variant. Graph: This graph shows the number of T cells per 106 peripheral mononuclear blood cells after two doses (red bars), of AstraZeneca in patients who received Moderna and a third dose (blue bars).
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. A further 13 Omicron cases were confirmed in Scotland. They are split between Lanarkshire, the Greater Glasgow-Clyde region and Lewisham.
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.
Laboratory tests for Covid PCR are used to determine if the test is positive. They look out for the spike protein, which can be found outside 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.
The majority of PCR tests carried out in England by labs that employ a detection kit to look for spike proteins and other components of the Covid cells are performed at least half the time.
In five days prior to November 28, the percentage of confirmed positive test results that did not detect spike protein rose from 0.1% to 0.3%.
The Covid cells are usually detected by these kits, although they can still detect other parts 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.
Omicron is causing an unprecedented increase in South Africa’s cases. Omicron was alerted to by scientists in South Africa who spotted the S gene dropout.
Experts have expressed concern about changes to the spike protein, raising concerns that this strain may not be protected by vaccines or natural immunity after an 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]Some cases were not available until a few days after the sequencing data was made.
‘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.’
NERVTAG is a government advisory committee on new and emerging respiratory virus threats. Today, it said that there were no Covid variants that could cause S-gene dropsout in South Africa.
All the S-gene Dropout Samples Sequencing in South Africa were confirmed Omicron Cases, making it ‘currently reliable’ as a marker for 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.
This comes as a result of data released by the National Institute for Communicable Diseases yesterday evening. It showed that 11,535 Covid cases had been recorded within the last 24 hours. That’s a 368 percent increase on the Thursday, when 2,465 new infection were reported.
The country had 51,402 Covid tests and 22.4% of those tested for the virus. Comparatively, 38.075 percent of the tests were taken last week on the same date and 6.5% were positive.
Figure: This graph illustrates the average percentage of test results that came back positive for South Africa in seven days and daily since the beginning of the pandemic.
Graph: Seven-day average of South African cases across provinces. Guateng, the epicenter for the Omicron wave is seeing an epidemic of infections (dark-green line).
Figure 1: This graph illustrates the average daily number of infection cases in South Africa over seven days since October. Guateng saw an epidemic of Omicron waves, with more than 1,000 infections per day.
In the meantime, hospitalisations increased by 180% in seven days. Last Thursday saw 98 patients admitted, and yesterday 274 Covid infected patients needed hospital treatment.
However, the number of Covid-related deaths has fallen from 114 on Wednesday to 44 today. This is a 61% decrease. Due to how long it takes for the virus to make you seriously sick, the trends in hospitalizations and deaths are often two to three week behind that of cases.
A preprint by researchers from Stellenbosch University near Cape Town suggests that Omicron has at most 2.4 times the chance of reinfecting someone.
Researchers from the government claim that there have been 35,670 cases of reinfections since the start of the pandemic. This is a significant drop in risk compared to last year’s first wave.
The risk of getting the virus from another person has increased to 2.4 for the first time.
The Stellenbosch university, in Cape Town, reported that Omicron may be able to bypass protection from an existing infection. This is unlike natural immunity which suppressed the Beta or Delta versions.
These experts stated that the data had important health implications especially for countries where there have been high infection rates in the past.
There are ‘urgent questions’ about Omicron’s ability to avoid vaccine protection, as well natural immunity. If so, how does this impact hospitalisations or deaths.
Simon Clarke, a microbiologist from Reading University said that the data were the first indication Omicron might be immune to previous Covid infections.
He stated that although they could not confirm Omicron’s reinfection as a fact, the researchers were able to establish that Omicron did not cause the increase in transmission of Beta and Delta variants.
“There’s no evidence to support the idea that this immune evasion occurs, though it may be caused by decreased antibody binding to Omicron’s mutated spike proteins.
He said, “Omicron has made a huge hole in the controversial argument we should allow the infection spread to try to build immunity.”
“Herd immunity, which seems now like nothing more than an idle dream. Omicron may have the ability to overcome vaccine-induced immunity. We are waiting for more information.
Researchers are at an all-time high speed trying to determine if Omicron has a higher transmissibility and death rate than other mutant strains. They say that reliable estimates could take up to a week.
Early reports in Southern Africa suggest that many cases are mild to completely unsymptomatic.
However, there is no evidence of an age breakdown. This makes it impossible to determine if the strain has spread to older individuals.
According to the WHO, it’s a mild strain. Christian Lindmeier spoke for the WHO today in Geneva. He said that he has not yet seen any reports about Omicron-related deaths.
“We’re gathering all of the evidence. We will discover more as we go.
“The more people we test, the more places… We will find more cases, more data, and hopefully, not only deaths, but more.”
Doctors in Norway have confirmed that 60 Omicron-infected people were at Christmas last week and are now experiencing mild symptoms.
The chief doctor for the affected district, Dr Tine Ravlo stated that the symptoms of the illness are similar to those reported in South Africa.
With 10-15 Omicron cases being confirmed using genetic sequencing technologies, only one case has been so far.
However, all cases can be assumed to have the same variant. Sequencing tests are expected to continue 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.
Ravlo stated that all the infections found in Oslo were traced back to the Christmas party, and there are no signs of a wider spread.
However, Dr Kall stated that she was skeptical about the claims of the new strain causing less severe diseases.
She wrote on Twitter: “I’m highly skeptical it could be milder. The best scenario is that it has the same severity as Delta… But you’ll notice milder symptoms today than Delta, since many people are now immune.
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.
The T-cells provide a longer lasting, more comprehensive protection than the antibodies. However, they are less effective at protecting against infection and can be used to treat autoimmune diseases.
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.
This comes just as Oliver Dowden, Tory Party Chairman, today urged people to ‘keep calm’ and continue with Christmas parties and plans despite Omicron. However, Britain’s bars, clubs, restaurants, and hotels that are already losing billions of pounds due to cancellations keep saying “the damage has already been done”.
Sky News’ Mr Dowden said that he believed the message was simple: Keep calm and continue with your Christmas plans. While we have put in place the restrictions, please keep your cool and go on.
“I am aware that there are concerns about the new version. This is why we took the steps that we already mentioned… and we believe that those measures are adequate at the moment. We recommend that people continue to follow their original plans.
In the midst of confusion over what to do next, some of Britain’s most important employers such as banks, tech and NHS decided to either cancel or move their festive celebrations online. Now, it is a 50-50 split.