Australia reveals key facts about Omicron doctors MUST know

Australia’s top doctors know the new Omicron variant of Covid-19 is transmissible but need more data to determine severity and whether it can evade vaccines.

The country has delayed the gradual re-opening of the international border until December 15 while experts scramble to answer these crucial questions. 

Early indications based on cases in South Africa, where the variant was identified on November 11, show the variant spreads quickly but is potentially less severe than Delta. 

In a press conference on Tuesday morning, Chief Medical Officer Paul Kelly said experts know the Covid-19 strain, which is the most mutated so far, is ‘transmissible’ because it passed between hotel rooms in Hong Kong.   

‘In terms of transmission on from those people, the only case we really know about is the one we talked about on Saturday in hotel quarantine in Hong Kong where there was someone who had come from southern Africa and transmitted to another person from another part of the world across the corridor. So we know it’s transmissible,’ he said. 

Health Minister Greg Hunt said the variant is ‘manageable’ and hoped the border re-opening will restart on December 15 as planned.

‘All of this is done on the presumption that we will recommence from 15 December but medical advice will guide our decision-making throughout,’ he said. 

The decision to pause the re-opening was made after a mammoth four-hour national security cabinet meeting of federal ministers on Monday evening.

Professor Kelly said he called for a ‘temporary pause’ while more data is gathered. 

‘This is a temporary pause so we can get the information we need, but we are committed to continue to reopen. That is the advice and decisions that were made at the NSC last night,’ he said. 

The South African province where the Omicron Covid-19 variant was first detected has suffered a more than 300 percent increase in virus related hospitalisations this week. 

But Professor Kelly said South Africa is not comparable with Australia because it only has a 25 per cent vaccination rate, while 87 per cent of Aussies are fully jabbed.  

At a separate presser in Melbourne, Victoria Premier Daniel Andrews said he will keep three day isolation for international arrivals in place ‘for a little while’ and said he has ‘no advice’ to move to 14-day hotel quarantine.

Cases of the South African strain in Australia grew to five on Monday with two more infections detected in international travellers who landed in Sydney over the weekend.   

Deputy Chief Medical Officer Dr Sonya Bennett said while it appeared the strain only causes mild illness, authorities may take weeks to figure out exactly how sick Australians could be if they catch the virus.

‘What we really want to know and what we should understand in the coming weeks is how severe the clinical illness is that is causes,’ she said on Tuesday.

‘[We also want to know] whether vaccines will continue to protect against that severe illness.

‘We don’t know enough about it yet but that is the sort of information we need to gather over the next few weeks.’

The new strain has about 50 mutations, of which 30 are on the spike protein.

Experts fear the variant’s level of mutation could make it unrecognisable to vaccines, which lock onto the proteins so the human body knows which cells to attacks.

Dr Bennett said the government hoped the new strain would not be as deadly as Delta – the strain that sent NSW and Victoria into months of lockdown earlier this year.

Despite the local surge in hospitalizations, South African officials insist that cases of the Omicron variant are generally mild compared to other strains. Pictured: A man suffers from a Covid infection in Cape Town, South Africa on December 29, 2020

‘It does appear to be a mild illness, particularly in vaccinated individuals, so that is reassuring,’ she said.   

The federal government has pushed back plans to bring in 200,000 foreign visa holders by two weeks until December 15 amid uncertainty about the new strain.

Deputy Chief Medical Officer Dr Sonya Bennett said while it appeared the strain only causes mild illness, authorities may take weeks to figure out exactly how sick Australians could be if they catch the virus.

‘What we really want to know and what we should understand in the coming weeks is how severe the clinical illness is that is causes,’ she said on Tuesday.

‘[We also want to know] whether vaccines will continue to protect against that severe illness.

‘We don’t know enough about it yet but that is the sort of information we need to gather over the next few weeks.’

The new strain – first reported by authorities in South Africa last week – has about 50 mutations, of which 30 are on the spike protein.

Experts fear the variant’s level of mutation could make it unrecognisable to vaccines, which lock onto the proteins so the human body knows which cells to attacks.

Dr Bennett said the government hoped the new strain would not be as deadly as Delta – the strain that sent NSW and Victoria into months of lockdown earlier this year.

‘It does appear to be a mild illness, particularly in vaccinated individuals, so that is reassuring,’ she said.  

A plan to bring in 200,000 foreign visa holders – who bolster the economy with tuition fees, fill labour shortages, and boost tourism – was to begin on Wednesday, but was postponed until December 15.    

Travellers wait in line verify Covid-19 vaccination status as they check-in for a flight to Sydney, Australia on Qantas Airways in Los Angeles on November 1

Pandemic-crippled industries relying on overseas tourists are now forced to wait until next month – at the earliest – for the much-needed boost they were expecting ahead of Christmas.  

Travel bubbles that were due to kick off between Australia to Japan and Korea have also been placed on the backburner for two weeks.      

The borders now only remain open to vaccinated Australians, permanent residents, immediate family, and ‘green lane’ travellers from New Zealand and Singapore, who were already allowed into the country. 

While the acceptance of ‘non-risk’ Australians is a blessing for many families expecting loved ones home for Christmas, people in eight southern African countries of concern will not be able to board flights. 

Flights cannot arrive from South Africa, Lesotho, Botswana, Zimbabwe, Mozambique, Namibia, Eswatini, or Malawi and anyone taking a roundabout route must quarantine for 14 days. 

Meanwhile, the South African province where the Omicron Covid-19 variant was first detected has suffered a more than 300 percent increase in virus related hospitalisations this week.

Gauteng, which includes the city of Johannesburg, recorded 580 hospitalizations because of the virus this week, per official data – a 330 percent jump from 135 two weeks ago.

Just under 40 percent of the provinces 12 million residents have received at least one shot of a COVID-19 vaccine – third-lowest of the nation’s 12 provinces.

Last week, the new Omicron variant was sequenced in 77 cases in the region, and many fear it is the most infectious strain of the virus yet and that it could evade vaccine protection because of its high number of mutations.

While South African health officials have reported that cases of the variant are often mild, the increase in hospitalizations in the province seems to hint otherwise.

Over the past two weeks, Covid related hospitalizations in the Gauteng province of South Africa have jumped 330% – from 135 in the week that ended on November 7 (week 45) to 580 last week (week 47). Gauteng is the province where the Omicron variant was first sequenced

Gauteng is the largest province in the country by population, as it is home to more than 12 million people.

After a Covid surge around three months ago, the province has experienced decreasing hospitalizations from the virus for weeks.

During the week that ended on November 7, 120 Covid related hospitalizations were detected.

Last week, that figure doubled to 276, before jumping to 580 last week.

Because genetic sequencing is only performed on a small percentage of positive tests, experts can not say which people have Omicron versus another strain. 

South African officials have said that cases of this new strain are relatively minor, though, to such an extent that it surprised them.

‘Their symptoms were so different and so mild from those I had treated before,’ said Dr Angelique Coetzee, a South African Medical Association board member, told UK newspaper The Telegraph.

‘It presents mild disease with symptoms being sore muscles and tiredness for a day or two not feeling well. 

‘So far, we have detected that those infected do not suffer the loss of taste or smell. They might have a slight cough. There are no prominent symptoms. Of those infected some are currently being treated at home.’ 

Joe Phaahla, South Africa’s health minister, has blamed the recent uptick in cases the nation has experienced on the highly infectious variant, though.

Over the past nine days, cases have increased nine-fold from around 500 per day on November 20 to 4,500 per day this week.

This surge in cases also corresponds with the surge in hospitalizations the nation has suffered in recent weeks.

One thing to note is that some of the 77 cases found by health officials last week were among vaccinated people – causing the alarm.

Vaccinated people generally have a lower risk of severe Covid infection than their unvaccinated peers, which could have resulted in the more mild cases.

Gauteng as a whole, though, has a vaccination rate of only 38 percent as of Monday morning, a low enough number that the province is vulnerable to surges of the virus. 

Gauteng has one of the lowest vaccination rates among the 12 South African provinces, with only 38% of the population having received the shots as of Monday morning. It is the nation’s most populous province

In response to the discovery of the new Covid variant, President Biden suspended travel from South Africa – and six of its neighbors – to the the U.S.

Many European nations, like the UK, have banned incoming flights from nations in the southern portion of the continent as well.

The move has been met with criticism from some health officials.

‘Travel restrictions may play a role in slightly reducing the spread of COVID-19 but place a heavy burden on lives and livelihoods,’ Dr Matshidiso Moeti, the World Health Organization’s regional director for Africa, said in a statement.

‘If restrictions are implemented, they should not be unnecessarily invasive or intrusive, and should be scientifically based, according to the International Health Regulations, which is a legally binding instrument of international law recognized by over 190 nations.

‘…The speed and transparency of the South African and Botswana governments in informing the world of the new variant is to be commended.’ 

‘WHO stands with African countries which had the courage to boldly share life-saving public health information, helping protect the world against the spread of COVID-19.’ 

Despite widespread travel restrictions, the variant has managed to find its way around the world anyways.

The UK has joined many European countries like Austria, Belgium, Czech Republic, Denmark, Germany, Italy, Netherlands, Spain, the UK and Portugal in finding cases of the variant over the past few days. 

Moderna CEO Stephane Bancel said Monday morning that it is likely too late to prevent the spread of the variant, and it probably has found its way into countries like the U.S. by now – it just has not yet been sequenced. 

Not much is yet known about the variant, but what experts do know has them terrified.

The variant has over 50 mutations, with 30 being on the spike protein, more than any other detected Covid variant.

Because available vaccines for Covid target the spike protein, these types of mutations could make the variant vaccine resistant.

Pfizer, BioNTech, Moderna and Johnson & Johnson – producers of the available vaccines in the U.S. – have all announced that they will either update their existing vaccine or release a stand along Omicron vaccine if needed.

BioNTech believes they will be able to determine the variant’s ability to evade the vaccines within the next two weeks.

So far, the variant has yet to reach America, and Dr Anthony Fauci, the nation’s top infectious disease expert, said he does not believe lockdowns are necessary.  

Why is Omicron so scary?

 What is so concerning about the variant?

Experts say it is the ‘worst variant they have ever seen’ and are alarmed by the number of mutations it carries.

The variant — which the World Health Organization has named Omicron — has 32 mutations on the spike protein — the most ever recorded and twice as many as the currently dominant Delta strain. 

Experts fear the changes could make the vaccines 40 per cent less effective in a best-case scenario.

This is because so many of the changes on B.1.1.529 are on the virus’s spike protein.

The current crop of vaccines trigger the body to recognise the version of the spike from older versions of the virus.

The Botswana variant has around 50 mutations and more than 30 of them are on the spike protein. The current crop of vaccines trigger the body to recognize the version of the spike protein from older versions of the virus. But the mutations may make the spike protein look so different that the body’s immune system struggles to recognize it and fight it off. And three of the spike mutations (H665Y, N679K, P681H) help it enter the body’s cells more easily. Meanwhile, it is missing a membrane protein (NSP6) which was seen in earlier iterations of the virus, which experts think could make it more infectious. And it has two mutations (R203K and G204R) that have been present in all variants of concern so far and have been linked with infectiousness 

But because the spike protein looks so different on the new strain, the body’s immune system may struggle to recognise it and fight it off.

It also includes mutations found on the Delta variant that allow it to spread more easily.

Experts warn they won’t know how much more infectious the virus is for at least two weeks and may not know its impact on Covid hospitalizations and deaths for up to six weeks. 

What mutations does the variant have? 

The Botswana variant has more than 50 mutations and more than 30 of them are on the spike protein.

It carries mutations P681H and N679K which are ‘rarely seen together’ and could make it yet more jab resistant.

These two mutations, along with H655Y, may also make it easier for the virus to sneak into the body’s cells.

And the mutation N501Y may make the strain more transmissible and was previously seen on the Kent ‘Alpha’ variant and Beta among others.

Two other mutations (R203K and G204R) could make the virus more infectious, while a mutation that is missing from this variant (NSP6) could increase its transmissibility.  

It also carries mutations K417N and E484A that are similar to those on the South African ‘Beta’ variant that made it better able to dodge vaccines.

But it also has the N440K, found on Delta, and S477N, on the New York variant — which was linked with a surge of cases in the state in March — that has been linked to antibody escape. 

Other mutations it has include G446S, T478K, Q493K, G496S, Q498R and Y505H, although their significance is not yet clear. 

Is it a variant of concern?

The World Health Organization has classified the virus as a ‘variant of concern’, the label given to the highest-risk strains.

This means WHO experts have concluded its mutations allow it to spread faster, cause more severe illness or hamper the protection from vaccines.

Where has the variant been detected so far? 

The variant has so far been spotted in five nations: South Africa, Botswana, Hong Kong, Israel and Belgium. 

Most cases have been spotted in Gauteng, a province in north east South Africa where Johannesburg is based.

The first case was uploaded to international variant database GISAID by Hong Kong and was spotted in someone who travelled to the country from South Africa.

No cases have been seen in the UK. But scientists do not sequence every positive Covid sample in the UK and not everyone who catches the virus will take a test.

This means there could be people infected with the variant in Britain.

What is the UK doing about the variant?

The Health Secretary announced last night six countries would be added to the red list from midday on Friday November 26.

The red-listed countries are: South Africa, Botswana, Eswatini, Lesotho, Namibia and Zimbabwe. This means all direct flights from these countries to the UK are banned.

Anyone arriving in England between midday today and 4am on Sunday from these countries — or who has been in the countries in the 10 previous days — must complete a passenger locator form, quarantine at home and should take a PCR test.

Anyone arriving from these countries after 4am on Sunday must stay in a managed quarantine hotel for 10 days and take a Covid test on or before the second day of their stay, as well as another test on or after day eight.

And the UK Health Security Agency classified B.1.1.529 as a Variant Under Investigation, which means it has worrying mutations.

Experts will now conduct a risk assessment and may increase its ranking to Variant of Concern if it is confirmed to be more infectious, cause more severe illness or make vaccines and medicines less effective. 

Where did B.1.1.529 first emerge?

The first case was uploaded to international variant database GISAID by Hong Kong on November 23. The person carrying the new variant was traveling to the country from South Africa.

The UK was the first country to identify that the virus could be a threat and alerted other nations. 

Since then, 77 cases have been confirmed in South Africa, two in Hong Kong and three in Botswana.

Health chiefs in Israel today announced it had one confirmed and two suspected B.1.1.529 cases, while there are two suspected cases in Belgium.

Experts believe the strain may have originated in Botswana, but continental Africa does not sequence many positive samples, so it may never be known where the variant first emerged.

Professor Francois Balloux, a geneticist at University College London, told MailOnline the virus likely emerged in a lingering infection in an immunocompromised patient, possibly someone with undiagnosed AIDS.

In patients with weakened immune systems infections can linger for months because the body is unable to fight it off. This gives the virus time to acquire mutations that allow it to get around the body’s defenses.

Will I be protected if I have a booster?

Scientists have warned the new strain could make Covid vaccines 40 per cent less effective.

But they said emergence of the mutant variant makes it even more important to get a booster jab the minute people become eligible for one.

The vaccines trigger neutralizing antibodies, which is the best protection available against the new variant. So the more of these antibodies a person has the better, experts said.

Britain’s Health Secretary, Sajid Javid, said: ‘The booster jab was already important before we knew about this variant – but now, it could not be more important.’ 

When will we know more about the variant?

Data on how transmissible the new variant is and its effect on hospitalizations and deaths is still weeks away.

The UK has offered help to South Africa, where most of the cases are concentrated, to gather this information and believe they will know more about transmissibility in two to three weeks.

But it may be four to six weeks until they know more about hospitalizations and deaths.

What is the variant called?

The strain was scientifically named as B.1.1.529 on November 24, one day after it was spotted in Hong Kong.

The variants given an official name so far include Alpha, Beta, Delta and Gamma.

Experts at the World Health Organization on November 26 named the variant Omicron.