Omicron is the WHO designation provided to a new Variant of Concern that has recently been detected in southern Africa.

The New Zealand Science Media Centre spoke to Professor Mike Bunce, Principal Scientist (Genomics), Institute of Environmental Science and Research.

Is Omicron more transmissible than Delta?

“It is too early to say. However, the fact that Omicron has been detected on a ‘background’ of Delta raises a flag. To determine how transmissible Omicron is relative to Delta will require (i) more testing to detect the variant and (ii) good epidemiology in areas where there are both Delta and Omicron circulating. Estimates of Omicron’s ‘R’ number will likely appear soon – this number will likely dictate the response of countries to this variant.”

How did Omicron evolve?

“Preliminary genomics suggest southern Africa as the source location. The genome that sits at the base of the Omicron tree is (currently) Botswana. We know from the genome it is very different to Delta. As many commentators have said, countries that sequence the genomes of cases, and are transparent with the results, should be thanked – these efforts are the early warning system the global community needs to act quickly to new potential Variants of Concern. Preliminary modelling suggests Omicron started to expand in southern Africa in September 2021.

Could this variant make our vaccines less effective?

“Again, too early to tell. The number of mutations in the spike protein will likely change the binding of some of our antibodies if challenged with Omicron. Other antibodies may continue to bind and offer protection. The same questions were asked in the Alpha to Delta transition. The salient question is if Omicron’s mutations within spike impact upon rates of hospitalisation and death – these will be the key statistics health providers will be seeking in coming days and weeks. An acid test of vaccine efficacy will be when Omicron encounters a country with high vaccine uptake. Will it gain a foothold?”

What is the risk of Omicron spreading to NZ?

“Each of the existing Variants of Concern has found its way to the NZ border, and it is likely that Omicron will also present at some point. Can it be contained at the border? The genomic surveillance net provided by ESR is a key piece of NZ’s detection strategy. As of the 27th Nov, we know Omicron has not yet presented at the NZ border – we can spot it relative to Delta as the genome looks very different.

“All but one Delta case (i.e. the index case in our current community outbreak) has 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.”

Will this affect NZ’s plans to loosen border restrictions in 2022?

“In light of Omicron’s arrival on the global stage it is prudent to keep a closer eye on the NZ border. This is the first action the government is taking. Sequencing the genomes of all border cases remains a priority. Retaining the MIQ system for international arrivals has given us options. I suspect there may be changes to the border in response to Omicron. There are options available depending on the risk – as new data is evaluated we will have a better understanding of the risk. As noted above, getting these decisions ‘right’ is a tough job.”

Will PCR test tracking of this variant be useful, especially if it spreads through countries that are not doing genomic testing at the same level as New Zealand?

“PCR testing remains a key strategy globally – It remains the most reliable test. It is unknown how the Rapid Antigen Tests will perform on Omicron – many tests in the market place (but not all) target the ‘N’ protein and not spike, so should continue to work.

“Finally, one piece of the ‘genetic tool kit’ that will help globally is a PCR test that fails to work with micron. This means if two (separate) PCRs are run on a single sample, and one fails, it likely indicates Omicron is present. This is a cheaper and faster way to detect the variant and will complement efforts to obtain whole genomes.”