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The rapid rise of Omicron — expert Q&A with ESR's Prof Michael Bunce

20 December 2021

Mask Covid Esr
Mask Covid Esr

The WHO has warned the Omicron Covid-19 variant is spreading at an “unprecedented rate” after being reported in 77 countries.

Each day researchers are learning more about Omicron, with the WHO saying it is likely to outpace Delta. Early studies show vaccines may have reduced effectiveness against the variant, but there are some promising results.

Professor Mike Bunce, Principal Scientist (Genomics), Institute of Environmental Science and Research (ESR), comments:

Do we know how Omicron evolved?

“This is still uncertain and may continue to be. The evolution of Omicron is likely to be either (i) an immune-compromised individual or (ii) an animal reservoir. The former is the favoured hypothesis. The genomics of Omicron came as a surprise to many working in the field as it looks as if the Alpha variant went into hiding (for about 12 months) and then reappeared with a new game plan.

“To complicate matters further, and in an ongoing evolutionary twist, there are two distinct lineages of Omicron (called BA.1 and BA.2). Through the use of genomics researchers are tracking both lineages as they gain a foothold around the globe. The complication for BA.2 is that the ‘simple’ PCR test often used for rapid detection of Omicron (called SGTF) does not work, meaning BA.2 might be flying under the radar. Using genomics, there remains a lot of scrutiny of Omicron and Delta including the possibility of the variants ‘merging’ (in a process known recombination) which can occur if infected with both variants at the same time.”

Is Omicron more transmissible than Delta?

“Both variants are highly infectious. Some preliminary studies (not peer reviewed) suggest that Omicron’s spike protein binds about four times as well to human cells (the ACE2 receptor) than the original ‘Wuhan’ variant and twice as well as Delta (study here). While it is still early days, and more experiments need to be run, the evidence to date suggest Omicron might have a more accurate key to our cells. This, coupled with its ability to dodge some antibodies, provides clues to why Omicron is causing a new wave of infection even in highly vaccinated countries like Denmark and the UK. Recent data (also not peer reviewed, reported here) suggests Omicron might be better at replicating in our upper airway (bronchus) than previous variants – this might aid in the spread of virus from person to person.”

How does Omicron evade the immune system and what are ‘breakthrough’ infections?

“Mutations in the viral gene that encodes the spike protein of the virus sit at the heart of any discussion surrounding immune system ‘escape’. The spike protein of all coronavirus variants differ – these differences impact the ability of our immune system, ideally primed with vaccines (or prior infection), to rapidly respond to new challenges such as Omicron. The ‘kick in the guts’ with Omicron is that unlike previous variants, there is evidence that the antibodies repertoire we build up aren’t quite as effective (e.g. study here).

“The good news is that, while reduced, these early studies still indicate some antibody binding. In addition, antibodies are not the only game in town – there is our cell-mediated immunity (T-cells) which can protect us too. Finally, there is some evidence that third/booster doses confer an added level of protection. In response to Omicron outbreaks the UK, Denmark and Australia have all recently shortened booster dose intervals to between three and five months. Accordingly, the Ministry of Health’s expert advisors are examining the evidence, need and timing here in Aotearoa for maximum protection and effect.

“With Delta we have still observed ‘breakthrough’ infections where vaccinated individuals can contract and pass on the virus. Mounting evidence suggests that with Omicron we will see a higher number of breakthroughs. It is a salient reminder that vaccines are not the only tool in the pandemic toolkit and we need to continue other infection measures e.g., mask use (you should be thinking of the swiss-cheese model of disease protection right now). Modified vaccines to tackle Omicron are already being developed, with time these may slot into the toolkit.”

What is the risk of Omicron spreading to NZ?

“Each of the existing coronavirus variants has found its way to the NZ border, it goes without saying that some have evaded our border defences. It seems it is only a matter of time before Omicron presents at the border – the hope is that it stays at the border. Every day ESR scientists are closely watching any border cases using genomic surveillance.

“Omicron data from highly vaccinated countries including UK, Denmark and Australia provides us, as a country, with the opportunity to evaluate infection data, hospitalisations and efficacy of interventions, and importantly make evidence-based decisions based on these data. The cautious ‘wait-and-see’ approach to COVID-19 has served us well throughout the pandemic and will likely be the case when grappling with Omicron.”

What about Omicron’s disease severity?

“I don’t see a lot of value in speculating about Omicron’s disease severity at this point in time. There are a lot of anecdotes and larger studies are just starting to appear (see here). Accurate commentary on disease severity requires a lot of carefully controlled data that take into account the many confounders that exist when trying to make direct comparisons of variants. For example; vaccine type/timing, boosters, previous infections, matched cohorts (e.g. age), better COVID-19 drugs, early diagnosis and season all impact on how the disease presents – it is not easy to disentangle all these factors.

“Even if Omicron (or another variant) result in half the hospitalisation rate, twice as many infections will place the same net demand on the hospital system. While the narrative that Omicron may be ‘less severe’ resonates with people it is worth remembering that the virus doesn’t care what makes us feel better. Assuming a lower disease severity may have poor public health outcomes if this proves not to be the case.”

No conflict of interest declared.