December 2, 2021

First graphic of Omicron's 32 spike mutations reveals why scientists are so worried about the most evolved Covid strain ever - but jury's still out as South Africa insists it's still only causing mild illness

• New images of Omicron highlight its 32 spike protein mutations, 25 more than the number in the Delta strain
• There are fears the variant could make vaccines, which target older versions of spike proteins, less effective
• But current reports from Africa indicate Omicron produces mild cases, with no evidence of jab dodging yet

by JOHN ELY SENIOR HEALTH REPORTER FOR MAILONLINE
dailymail.co.uk

This is the image that has sparked fear among scientists, prompted ministers to turbocharge the UK's booster vaccine rollout and seen the return of mask mandates in England.

It details the new super-mutant Omicron variant's 32 spike protein mutations which experts fear will make it the most infectious and vaccine-resistant strain yet.

The graphic, released by the country's top variant monitoring team, also lays bare how it is far more evolved than even the world-dominant Delta strain, with nearly five times as many alterations on the spike.

As of yesterday, just 32 cases of Omicron have been detected in the UK but hundreds are expected to emerge in the coming days and there are signs it is spreading domestically already.

The new strain shares mutations with all of the main 'variants of concern' — including Alpha, Beta and Delta — but has dozens more which all point to heightened transmissibility and vaccine escape.

The stark image comes after Norway announced 60 people likely contracted Omicron at a single Christmas party at a seafood restaurant in Oslo, in what is likely to be the world's biggest outbreak of the new strain so far.

The new image, which was was released by the Covid Genomics UK Consortium (COG-UK), shows three mutations — H655Y, N679K, and P681H, located in the lower right of the image — that could help the virus sneak into the body more easily.

UK Government experts originally said they believe existing vaccines would be made at least 40 per cent weaker at preventing infections from the new strain.

This is because current jabs were designed to recognise the spike protein of the original virus that emerged in China, which looks significantly different to Omicron's.

Concern over the variant's potential as a super-spreader prompted No10 to turbocharge the rollout of Covid boosters, ban travelers from several African nations, and reintroduce compulsory mask wearing.

But there are contradictory reports on whether Omicron causes mild or severe illness and what impact it will have on vaccine effectiveness. Scientists won't know for sure until another three weeks, when they can isolate the virus in a lab and expose it to the blood of previously infected, or vaccinated, people.

Southern African health officials and the World Health Organization have indicated most cases are only resulting in mild disease, and insist there is no evidence existing vaccines are any less effective. (This suggests that the new virus could be a godsend. If it produces mild disease but generates Covid-19 immunity, it is exactly what humanity needs. - De)

However, cases in South Africa have increased meteorically to 8,561 cases per day, soaring six-fold (571 per cent) compared to 1,275 a week ago, shortly after the country alerted the world to the emergence of Omicron.

Hospitalisations in the country have also more than doubled in the last two weeks, from an average of 86 per day to 184.

And now fears that Omicron is more infections than Delta appears to be true, since the virus is spreading with such ease in South Africa where natural immunity is about 80 per cent. Israeli health authorities have also reported Omicron is 30 per cent more infections than the Delta strain.

And N501Y, which was previously seen on Alpha, Beta and Gamma, also helps the virus bind to the body's cells more easily, allowing for it to enter the body and replicate more efficiently.

Meanwhile, it has 26 mutations on its spike protein — that haven't been seen in previous variants and scientists are still probing whether they will have any impact on how fast it can spread.

It comes as a Christmas party at the Louise seafood restaurant in Oslo saw up to 60 people contract Omicron in what is likely to be the world's biggest outbreak of the new strain so far.

Norwegian epidemiologists have ruled out the possibility the infections are Delta variant cases and said there was a 'high probability' it was Omicron because at least one of the Scatec employees had recently returned from the renewable energy company's South African office in Cape Town.

And in another twist, Scatec has insisted only vaccinated employees were allowed to attend the Christmas party last Friday and they needed a negative test result beforehand.

One of the company's super-spreaders was also drinking in an Irish bar in the city the following night, raising fears more could be infected.

More than 71 per cent of Norway's population are fully vaccinated, higher than the 69 per cent of Brits and 59 per cent of Americans who have had both jabs.

Professor Anne von Gottberg, a clinical microbiologist at South Africa's national health agency, told an emergency World Health Organization conference today it 'does look like there is a predominance of Omicron throughout the country'.

While the vast majority of Omicron cases have so far been reported as mild, there are concerns this perception is flawed due to the majority of cases in South Africa being seen in people about 30-years-of-age, who are statistically at less risk of sever Covid illness than older age groups.

Professor von Gottberg said scientists are worried about the number of Omicron cases that are being spotted among people who have previously had Covid, compared to the reinfection rate during the Beta and Delta-fuelled waves.

But she said the virus may be no more transmissible than Delta, the illness it causes is thought to be 'less severe' and vaccines should protect against illness.

The jury is still out on Omicron's impact on vaccine effectiveness, but Israeli health chiefs raised hope this week by claiming people who get a booster Pfizer Covid vaccine or who had their second jab within six months should still be highly protected against Covid.

But experts warn current findings are anecdotal and it will take two weeks before they can test how the virus performs in laboratories.

The variant has been spotted in 28 countries worldwide and is likely to have been spreading for weeks before South Africa raised the alarm. The Netherlands detected a case one week earlier, while Nigeria found its first case in a sample taken in October.

It was even in the UK before it was first spotted by scientists last week, with nine cases in Scotland on November 20, causing speculation the strain was imported from the COP 26 climate conference or a rugby game at Murrayfield Stadium against South Africa.

The extent of Omicron's spike protein mutations is what has prompted concern that it could effectively dodge the protection offered by the Covid vaccines.

This is because the jabs are designed to train the human body's immune system to identify the spike protein of the original Covid virus so it can immediately mount a defense.

But if a Covid variant were to emerge with sufficiently divergent spike proteins from its ancestor, vaccines would be less effective as the body would not recognise the new virus strain as an immediate threat.

Whether Omicron is this long-dreaded vaccine dodging variant is still unclear.

It is expected to take scientists a few weeks to determine how exactly Omicron interacts with the current crop of vaccines through running tests with a live sample of the virus and blood samples taken from vaccinated individuals.

Omicron has other mutations not included in the COG-UK image, two in its nucleocapsid protein and one it is membrane protein which could make it more infectious.

Some 42 cases of Omicron have been detected in the UK, and although though none of these cases have required hospitalisation the vaccination status of the infected individuals is unknown.

In reaction to the emergence of the Omicron, Boris Johnson this week set a target of offering more than 50million booster jabs to every adult by the end of January.

The Government has also drafted 400 army medics and 1,500 pharmacies into the behemoth booster campaign in an effort to turbocharge the pace of the rollout.

But whether Omicron is as scary as is being made out to be is in question with the World Health Organization stating yesterday that most cases of the variant are 'mild' or show no symptoms at all.

A spokesperson for the global health agency said early data suggests the mutant strain is better at infecting people than Delta, even the fully vaccinated.

But there is no signal that existing vaccines will be any less effective at preventing hospitalisations and deaths, the official, speaking anonymously, told Reuters.

It is unclear what evidence the WHO was referring to, but the comment marks the first official hint that the Omicron super-strain may not wreak as much global havoc as initially feared.

But there has been concerning news from South Africa, which first alerted the world to the emergence of Omicron last week.

Professor von Gottberg, from the National Institute for Communicable Diseases (NICD), said 183 of the 249 cases that have been sequenced in South Africa this month have been caused by the super strain.

But experts warn it will be at least two weeks until they have a better understanding of what impact the variant could have.

Dr Maria Van Kerkhove, an epidemiologist at the WHO, said 'surveillance bias' could be underestimating the severity of Omicron, because young people have been the main spreaders of the strain.

And SAGE, No10's scientific advisors, warned Britain should brace for a 'potentially very significant wave with associated hospitalisations' this winter if the worst estimates about Omicron turn out to be true.

Cases have been soaring in the country since the super mutant Omicron variant emerged, with experts stating the variant appears to be more infectious than Delta and has mutations that may allow it to dodge vaccine protection.

South African scientists said the strain was 'rapidly becoming dominant' in a briefing on the new figures, adding: 'The mutation profile and epidemiological picture suggests Omicron is able to get around some of our immune protection (to cause infection) but the protection against severe disease and death from vaccines should be less affected.'

Data from the National Institute for Communicable Diseases (NICD) shows 11,535 new Covid cases were recorded in the last 24 hours, a jump of 368 per cent on last Thursday when 2,465 new infections were registered.

Cases have been soaring in the country since Omicron emerged, which experts say appears to be more infectious than Delta and has mutations that may allow it to dodge vaccine protection.

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, Covid hospital admissions nearly tripled in a week, but deaths have fallen 64 per cent.

The 11,535 new infections recorded in South Africa brings the country's total throughout the pandemic to 2.9million.

Nearly a quarter of all those who took a Covid test were positive for the virus.

A third of all cases in the country are concentrated in the north eastern Gauteng province, the epicentre of the Omicron outbreak.

Meanwhile, 17.4 per cent of the infections were recorded in each of KwaZulu-Natal, in the east of the country, and Northern Cape, in the north west.

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 today.

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.

Scientists in South Africa have warned that the vast majority of people who end up being hospitalised with the Omicron variant are unvaccinated.

Some 23.8 per cent of South Africa's entire population is double-jabbed, compared to 67.9 per cent of Britons and 58.1 per cent of Americans, according to Our World in Data.

But South Africa is still recording far fewer overall Covid cases per population size than both the UK and US.

And so far, only 172 Omicron cases have been confirmed in South Africa and doctors there maintain that patients with the new variant are presenting with milder symptoms than previous strains — even though daily cases have soared.

The figure rose to 4,373 on Tuesday, with 10.2 per cent of those swabbed testing positive.

The upward trend continued yesterday, with 8,561 testing positive — increasing six-fold in a week and nearly doubling on Tuesday's number — equating to a positivity rate of 16.5 per cent.

Professor von Gottberg said about 75 per cent of samples that have been sequenced are Omicron, but she noted there is a lag, due to the time it takes to collect and sequence positive tests.

And the number of positive samples sequenced — when scientists examine a positive sample in a laboratory to determine what Covid strain caused an infection — in South Africa in November equate to less than one per cent of positive cases for the month.

Professor von Gottberg said: 'However, it does look like there is a predominance of Omicron throughout the country and Omicron has been identified through sequencing in at least five of our provinces that have sequencing data.

'And we think the other provinces were just not identifying it yet, because we don’t have specimens that have been sequenced for those provinces.'

And she warned that scientists are worried about the number of Omicron cases that are among people who have previously tested positive for Covid.

South Africa has a testing database that matches positive PCR and antigen tests to people so it can count reinfections — which it defines as a positive test from an individual 90 days after they first test positive.

Professor von Gottberg said: 'We monitored these reinfections for the Beta and for the Delta waves and we didn’t see an increase in reinfection over and above what we expect when the force of infection changes, when the wave stops.

'However, we are seeing an increase for Omicron. And that sort of speaks to that fact in our population with a high seroprevalence — so where many people have that previous infection — we believe that that previous infection does not provide them protection from infection due to Omicron.

Meanwhile, Israeli health minister Nitzan Horowitz yesterday said there was 'room for optimism' about the variant and existing vaccines will shield against severe illness from the super-strain, based on 'initial indications'.

Hours later, a report by an Israeli news channel claimed the Pfizer jab was 90 per cent effective at preventing symptomatic infection from Omicron, only slightly less than Delta.

The Channel 12 news broadcast also claimed the super variant is just 30 per cent more infectious than Delta — much lower than initially feared.

For comparison, Delta is 70 per cent more infectious than the Alpha strain, which it outpaced earlier this year.

http://www.dailymail.co.uk/news/article-10267387/Shocking-graphic-Omicrons-mutations-reveals-scientists-worried.html

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