Scientists have spotted another ‘sister’ lineage of the super-mutant Omicron Covid variant.
A South African man in Queensland who tested positive for Omicron has a genetically different version of the virus that experts have dubbed ‘Omicron Like’.
The man, who returned from the Omicron epicenter South African province of Gauteng last week, is isolating at a Brisbane hotel quarantine facility and is understood to have a mild case of Covid.
Queensland’s health minister Yvette D’Ath confirmed the case meant Omicron has now been classified into two lineages by the international committee.
‘We are standing here announcing a new version of Omicron and it’s a first in the world,’ she said.
Cases of Omicron-like are also being reported in South Africa and Canada though none have yet been reported in the UK.
While information is still emerging, one key difference of Omicron Like is that the new sister lineage is missing a genetic quirk used by health officials to track the spread of the original super-mutant strain.
Known as the S gene dropout, this aspect of Omicron meant it can be detected using a relatively simple PCR test, as opposed to more complicated lab tests.
The fact that Omicron Like does not have this S gene dropout means this shortcut cannot be used, meaning it will be harder to track as an outbreak.
There is no information currently on if Omicron Like is any more, or even less, infectious or if it has the potential to impact on vaccine effectiveness, though it has fewer mutations than original Omicron.
Queensland has recorded two cases of the Omicron Covid-19 variant but health authorities say there are differences between them (pictured travellers at Brisbane Airport)
Health Minister Yvette D’Ath (pictured) confirmed Omicron has now been classified into two lineages by the international committee, and both have been detected in Queensland
Queensland’s Chief Health Officer Peter Aitken said experts were able to distinguish between the two types of Omicron genetically.
‘[They] recognised there are differences between the full and normal Omicron classification, passed it on to the international committee in a really quick time frame,’ he said.
What do we know about ‘Omicron Like’?
Not much, apart from being genetically distinct from the original Omicron, how these differences could effect the infectiousness or severity of infection of the virus is unclear.
In summary, Omicron Like appears to be less mutated than Omicron, having 14 mutations as opposed to 32.
It should be noted this is still however, twice the number of mutations found on the currently dominant Delta variant.
One key difference between the two Omicrons is the S gene dropout.
This quirk of Omicron, where a particular gene is absent, made it quick to detect in a PCR test, making tracking Omicron outbreaks easier.
Omicron Like does not possess an S gene dropout, meaning it could fly under the radar of PCR testing, instead appearing as Covid.
While this means a person with Omicron Like will still test positive for Covid we won’t immediately suspect its a case of Omicron, potentially making tracking an outbreak, and learning more about it, slower.
In terms of transmissibility, we know Omicron is more infectious, and Omicron Like could share these same qualities.
Debate is still ongoing on how severely ill Omicron could make people but preliminary data is that it produces ‘milder’ cases of Covid.
But it could still be dangerous from a public health perspective as its higher transmissibility could see more people needing hospital care with a subsequent impact on health services.
‘This now led to a re-classification of Omicron.
‘It (Omicron Like) has enough genes to be classified as Omicron, but we don’t know enough about it for what that means as far as clinical severity, vaccine effectiveness.
‘What we do know is that Omicron is more infectious and more transmissible.’
When identifying the original Omicron variant, labs have indicated that when using PCR tests, one of three target genes is not detected.
This is known as S gene dropout which the new sub-lineage does not have, Dr Aitken said.
The S gene dropout is one the quickest ways to track Omicron cases as a comparatively simple PCR test can identify it, rather than having to rely on more complex methods.
The fact that ‘Omicron Like’ doesn’t have the S gene dropout makes it harder to initially detect and therefore track as a specific outbreak.
‘Normal’ Omicron has about 30 different gene changes, while the new sub lineage has about 14.
The arrival of Omicron Like in Queensland came as the Australian state recorded its first case of the original Omicron variant as well.
Queensland health officials said they are expecting a ‘difficult period’ ahead with more cases to come.
Meanwhile in the UK, ‘Professor Lockdown‘ Neil Ferguson today refused to rule out another nationwide shutdown to tackle the Omicron super variant as he warned that it will be dominant before Christmas.
The Government scientist, whose modelling bounced No10 into the original lockdown last spring, said the return of stay-at-home orders ‘certainly might be possible’ if the mutant strain threatens to overwhelm the NHS.
He told the BBC Radio 4 Today programme: ‘There is a rationale, just epidemiologically, to try and slow this down, to buy us more time principally to get boosters into people’s arms because we do think people who are boosted will have the best level of protection possible, but also to buy us more time to really better characterise the threat.’
It is unclear how the British public would react to fresh social restrictions over Christmas, after allegations surfaced this week that Boris Johnson held a rule-breaking lockdown party in Downing Street last December, when millions of Britons were unable to visit loved ones.
There are growing concerns about festive freedoms after the total number of British Omicron cases rose to 437 yesterday, with the highly evolved variant now in every country in the UK and almost every region of England.
But experts warn thousands of cases are flying under the radar because not all samples are analysed for variants and Omicron is estimated to be doubling every two or three days — much faster than when Delta exploded on the scene.
Eminent epidemiologist Professor Tim Spector claimed infections of the highly evolved variant were doubling every two days. The above graph shows how the number of daily cases of Omicron could breach the 100,000 barrier before New Year’s Day, if that pace continues
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
According to reports, No10 is already drawing up new plans for Britons to work from home and for offices to be closed in an attempt to avoid bringing in last-minute Christmas curbs. One source said Mr Johnson was given a ‘sobering’ briefing by his chief scientists yesterday in an effort to soften up ministers for tougher curbs.
Ministers are due to review the current suite of anti-Omicron measures — compulsory masks and stricter travel testing — on December 18, which has raised fears that Britons could be stung by last-minute curbs just days before Christmas.
Professor Ferguson said light measures like WFH ‘wouldn’t stop it but it could slow it down’ and buy the country precious time, extending the doubling time to five or six days. ‘That doesn’t seem like a lot, but it actually is potentially a lot in terms of allowing us to characterise this virus better and boost population immunity,’ he added.
Omicron cases are concentrated in London and in Scotland. As Britain’s major transport hub, London has often been the UK’s epicentre for new variants. But Professor Ferguson claimed Omicron might have been seeded in Glasgow at the Cop26 climate summit at the start of November in Glasgow.
The Imperial College London scientist said that while Omicron was concerning, it is still unclear what impact it will have on severe disease, hospitalisations and deaths. The first lab study of the super-variant in South Africa last night found that people given two doses of Pfizer’s vaccine produce forty times less antibodies when exposed to Omicron.
Professor Ferguson said the finding suggests Omicron will cut the effectiveness of current vaccines on mild disease in half, but he said they should still hold up against severe illness.
Pfizer vaccine provides FORTY times fewer antibodies to fight Omicron than it does other Covid variants, study finds
The Pfizer-BioNTech COVID-19 vaccine could be significantly less effective against the newly discovered Omicron variant that it was against previous strains of the virus.
Researchers at the African Health Research Institute (AHRI) found that there are forty times less antibodies in Pfizer vaccine recipients that can fight Omicron than there are for other variants.
The pre-print study, made available Tuesday pending peer-review, implies that the vaccine could be less effective against the strain detected last month in South Africa.
Conclusions from it cannot yet be drawn, though, and researchers are not yet sure how much more likely the Omicron variant is to cause infection in a vaccinated person than other strains are.
The new variant has been detected in at least 19 U.S. states and nearly 50 countries worldwide as of Tuesday night, and is feared to be the most contagious strain of the virus yet.