Travellers queue at OR Tambo's airport in Johannesburg, South Africa. Many countries have placed new travel restrictions on southern Africa following the detection of Omicron. Photo / AP
The world is facing the prospect of yet another new Covid-19 threat in the freshly designated "variant of concern", Omicron. What do we know about it so far? And what troubling questions does it raise about the pandemic's future? Science reporter Jamie Morton explains.
Within days of its detection in southern Africa this month, the coronavirus variant B.1.1.529 - which we now know better as Omicron – gave scientists two reasons to worry about a major new threat.
One, the variant was found to be responsible for the bulk of virus samples collected over a week in South Africa's Gauteng province – capital Johannesburg – where there's been a sharp rise in Covid-19 cases.
And two: the freakish nature of Omicron itself.
We know that new variants are created as a virus makes "mistakes" - or mutations - while copying its own genome to replicate and spread.
If one of these mutations happened to offer some advantage, like more easily invading cells, then it became more likely that it increased in frequency.
In the Sars-CoV-2 virus that causes Covid-19, most of these mutations tended to occur within the virus' distinctive "spike protein", which it used to recognise and gain entry to our cells.
Such mutations have been troubling signatures of the variants that have come before – Alpha, Beta, Gamma and Delta among them – and some of these have aided the virus in spreading faster.
In Omicron, however, scientists have counted around 50 mutations, and more than 30 within its spike protein alone – about double that of Delta.
Not only did that signal the potential to infect more people, but also to develop more mechanisms with which to escape immunity, given most Covid-19 vaccines work by forming antibodies against the spike protein.
On November 26, it became the World Health Organisation's (WHO) fifth "Variant of Concern" - and was soon confirmed in countries across five continents.
WHO update on Omicron, the new #COVID19 variant of concern: What we know & what we don't https://t.co/OVSKb74pHd
— World Health Organization (WHO) (@WHO) November 28, 2021
University of Auckland senior lecturer Dr David Welch figured that, because large numbers of cases had so far only been found in southern Africa, the variant must have been present for some time - maybe several months - to reach its current outbreak size.
"It is likely there is local spread in many regions already, if only at low levels currently."
In its latest update, the WHO said it still wasn't yet clear whether Omicron was more transmissible than other variants – including the globally dominant Delta.
"The number of people testing positive has risen in areas of South Africa affected by this variant, but epidemiologic studies are under way to understand if it is because of Omicron or other factors."
One such factor was something called the "founder effect", which occurred when there was a selection of initial genetic patterns that dominated observed cases.
That didn't necessarily mean the virus itself was more transmissible – and could just mean scientists were selectively learning about the infection from a subset of people infected with one particular strain, University of Canterbury epidemiologist Associate Professor Arindam Basu said.
"Having said that, and given what we know about Delta, it is likely that Omicron strain will enable the virus to propagate fast in populations," Basu added.
"The effective reproduction number [the average number of infections caused by a single case] is likely to be higher than that of Delta. That then will have the undesirable effect of fast transmission."
Genomic surveillance of COVID-19 in NZ (thanks @ESRNewZealand ) enables us to rapidly see what variants of the virus are circulating here & overseas. Graphic by @Jemma_Geoghegan is an overview of NZ delta cases compared to Omicron - with many new mutations - not yet seen in NZ. pic.twitter.com/vL8G3AO4l2
— NZ ChiefSciAdvisor (@ChiefSciAdvisor) November 27, 2021
Professor Mike Bunce, a principal scientist at ESR, said finding this out would require more testing to detect it - and good epidemiology in places where both Omicron and Delta were circulating.
Once Omicron's R value was published - early indications suggest a figure of nearly two in Gauteng - countries could determine how they would respond.
Many have already taken pre-emptive steps, such as New Zealand's weekend move to add South Africa and eight other southern African nations to its "very high countries" list.
That meant that only New Zealand citizens could travel here, with two weeks in MIQ required on arrival.
Bunce pointed out that each of the other variants of concern had found their way to our border – and it was likely Omicron, too, would turn up at some point.
Because ESR scientists were sequencing the genomes of all positive cases confirmed at the border, it would be quickly detected when it did.
He added that all but one Delta case – the "index case" that ignited our current community outbreak – had been contained at the border thanks to our MIQ system.
"The ability to contain a challenge by Omicron will depend on how infectious it is - and the effectiveness of other measures including: pre-departure tests, vaccine travel requirements and mask mandates."
Bunce said further testing would also tell us more about how vaccines like the Pfizer shot performed against the variant.
In other strains, two doses of the Pfizer vaccine have been shown to slash the risk of symptomatic illness by between 64 and 95 per cent – and severe illness and hospitalisation by 90 to 96 per cent.
"The number of mutations in the spike protein will likely change the binding of some of our antibodies if challenged with Omicron," he said. "Other antibodies may continue to bind and offer protection."
The very same questions were asked when Delta overtook Alpha – and Pfizer's vaccine had held up.
Massey University's Professor Nigel French believed the vaccine could be just as effective against Omicron.
"Evidence suggests that vaccination, particularly if you have had two or more shots, will produce antibodies that will neutralise new variants."
Pfizer has told Reuters it would be assessing information collected over the next two weeks, and, if a modified vaccine was required, one could be ready to ship in just 100 days.
Whether existing drugs, such as antiviral and monoclonal antibody treatments, worked against Omicron was now also urgently being assessed.
Bunce felt the salient question would be whether Omicron's spike protein mutations translated to higher rates of hospitalisation and death – something that hadn't been seen so far.
"These will be the key statistics health providers will be seeking in coming days and weeks."
An acid test of vaccine efficacy, he added, would be whether Omicron was able to gain a foothold in a highly vaccinated country like New Zealand.
Welch expected that, if vaccines did prove less effective at blocking transmission, it would be the unvaccinated among us that would be most affected, given case numbers, and thus the chance of exposure, would be much higher.
"Getting vaccinated remains the best defence any individual can take against the virus."
As it stood, he said there could be a benefit in delaying its arrival through keeping up border restrictions such as MIQ requirements for longer than currently planned.
"The time bought by this could be used to vaccinate 5-to-11 year olds, increase vaccination rates across the whole population, and provide booster shots to people who are five months or more past their initial two doses," he said.
"This would better prepare us for its arrival."
New coronavirus variants became an inevitability from the moment the parent strain or so-called "wild type" of Sars-CoV-2 was unleashed upon the world late in 2019.
While others such as Lambda have gained attention, none have yet managed to outperform Delta, which has been able to spread about twice as quickly as the wild type.
That's led to some speculation that Delta could ultimately be the virus at "peak fitness" - or the variant that we'll be stuck with.
Otago University virologist Dr Jemma Geoghegan said that, while Delta continued to spread effectively among countries with large numbers of susceptible hosts, the selection pressure could shift as it began encountering higher levels of immunity from vaccines or past infection.
"So, we're still effectively in an evolutionary arms race, with host and virus constantly trying to out-compete each other."
Because this pandemic was without precedent, scientists have been reluctant to offer predictions about its long-term course.
But one widely cited report by the UK Government's Scientific Advisory Group for Emergencies (SAGE) set out four scenarios.
They included a "super-variant" that emerged to ravage the world population with severe disease; a drug-resistant variant created as a direct result of anti-viral strategies; a variant that evolved to evade vaccines, perhaps through "reverse zoonosis", where humans infected animals with the virus before it bounced back to us.
The fourth was a variant that spread faster and became endemic, but which came with much milder infection in most people, just like human coronaviruses that cause common colds.
"You might have something that's horribly virulent and spreads quite well, but then you might have another variant that's much less virulent, but spreads very, very well - and this then becomes the dominant one," Welch explained.
"So, I've already heard a couple of people say that, wouldn't it be great if Omicron is actually less virulent but spreads more easily? Of course, it's way too early to even discuss that."
Geoghegan said it was nonetheless "quite shocking" to see the sheer number of mutations folded within Omicron.
The unusual combination has led many scientists to suggest the variant may have arisen from a chronic infection of an immunocompromised patient such as a person with HIV/Aids, which continued to wreak havoc across Africa.
Importantly, it also wasn't just the number of individual mutations that mattered but how they all worked together.
"Is this the one we all have been afraid of? That is, a highly transmissible, vaccine escape, more virulent variant?" Otago University virologist Professor Miguel Quiñones-Mateu said.
"Personally, I think it will be difficult for the virus to evolve or select for this trifecta.
"However, having a canvas of eight billion people to explore, who knows, it may be just a matter of time."
