The heavily-mutated Covid-19 variant Omicron is spreading in South Africa as the country sees a fresh spike in cases.
Early evidence suggests there is an increased risk of re-infection with Omicron (previously reported in media as the Nu variant, or B.1.1.529). The variant can be detected using a ‘widely-used’ type of PCR test, without having to do genomic testing.
The SMC asked experts what we should know about the new variant.
Associate Professor Siouxsie Wiles, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland:
Associate Professor Wiles has written an explainer for The Spinoff.
Dr David Welch, Senior Lecturer, Centre for Computational Evolution and School of Computer Science, University of Auckland, comments:
Is Omicron more transmissible than Delta?
“It is not yet clear that it is. Various possibilities include that there were some super-spreading events involving this variant which gave its numbers an initial boost in a susceptible population; that it is able to spread more easily to people who have some sort of immunity (either from vaccination or previous infection) more easily than Delta can; or, that it does actually spread faster than Delta in any population. As experiments are run and we observe what is happening over the next few weeks, we will be able to answer this question more precisely. In the meantime, we should be preparing for the possibility that it will spread faster than Delta.”
Could this variant make our vaccines less effective?
“There are various ways of measuring vaccine effectiveness: the primary measure is whether it prevents serious disease and death. There are good reasons to think that vaccines will still be effective against Omicron in preventing serious disease and death.
“Other measures of vaccine effectiveness are whether it stops people getting infected or whether it stops people transmitting the virus to others when infected. There are signs in Omicron’s collection of mutations that vaccines may be less effective at preventing infection. Whether onward spread is also more likely at that point remains to be seen.
“If the vaccines are less effective against Omicron at preventing infection and transmission, the unvaccinated in our population will likely be the ones who are most affected as case numbers will be higher and everyone will have a higher chance of being exposed to the virus. Getting vaccinated remains the best defence any individual can take against the virus.”
What is the risk of Omicron spreading to NZ?
“Currently large numbers of cases of Omicron have only been found in southern Africa. It must have been there for some time to reach the current outbreak size and various cases have been found elsewhere around the world in people with travel connections to southern Africa. It is likely there is local spread in many regions already, if only at low levels currently.
“As with all other variants, we can expect Omicron to arrive in Aotearoa at some point. 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 5-12 year olds, increase vaccination rates across the whole population, and provide booster shots to people who are 5 months or more past their initial two doses. This would better prepare us for its arrival.
“With all arrivals to Aotearoa still going through MIQ, being tested, and having their genomes sequenced if found to be infected, we are likely to be able to detect it and prevent its introduction for the time being.”
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?
“Yes, this is useful. Genomic sequencing is much slower and more laborious than simple PCR tests so this simple test will provide a lot of data about Omicron’s spread that we wouldn’t otherwise have.”
Conflict of interest statement: “David Welch is currently contracted to provide advice to MoH on the genomics of the current outbreak.”
Professor Mike Bunce, Principal Scientist (Genomics), Institute of Environmental Science and Research, comments:
“Omicron is the WHO designation provided to a new Variant of Concern that has recently been detected in southern Africa. There is only limited information on Omicron, but lots of speculation. We have lots of questions about this variant but only limited answers. Our decision makers need to carefully weigh up the evidence as they have done throughout the pandemic – it is not an easy job.”
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. The tree produced by Jemma Geoghegan illustrates this graphically (click to see full size):
“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.”
No conflict of interest declared.
Professor Nigel French, Co-Director, One Health Aotearoa, comments:
Is Omicron more transmissible than Delta?
“This is still the subject of ongoing investigation and we will know more in the coming days and weeks as more epidemiological and experimental data become available.”
Could this variant make our vaccines less effective?
“The current vaccines are still likely to afford valuable protection against new emerging strains, and could be just as effective against Omicron as for other variants. Evidence suggests that vaccination, particularly if you have had two or more shots, will produce antibodies that will neutralise new variants. This will not only protect you against infection and serious illness, but also reduce the likelihood that you will transmit infection to others – vaccination remains key to protecting yourself and others around you. Importantly, other public health measures are also likely to be just as effective against the new variant – including mask wearing, distancing, avoiding large crowds, testing, handwashing, using the Covid tracer app, and isolating when ill. Keeping up our vigilance and taking those everyday measures that we’re so used to now, will help protect us against Delta, Omicron or any other variant that may emerge in the future.”
What is the risk of Omicron spreading to NZ?
“We don’t know how rapidly or how far this strain will spread, but by constantly monitoring the situation globally and adopting risk-based measures we will be well-prepared to prevent, or at least delay, it crossing our border, and to manage community transmission should it occur. In the meantime, continuing to increase the level of protection afforded by vaccination as well as maintaining testing and genome sequencing of cases in MIQ and in the community, will help to mitigate the risk.”
Will PCR test tracking of this variant be useful?
“Rapid, cheaper tests are highly valuable, particularly in lower resource settings, and a test that could be used more widely to track emerging variants of concern, would help early detection and management of outbreaks. We are fortunate in NZ to have widespread application of genome sequencing. Although more expensive, this provides information at a much higher resolution, which is more useful for tracking the source of local and long-range transmission, and assisting more targeted control measures.”
Conflict of interest statement: “Member of the Ministry of Health COVID-19 Technical Advisory Group”
Associate Professor Arindam Basu, College of Education, Health & Human Development, University of Canterbury, comments:
Is Omicron more transmissible?
“Not necessarily, as we may be seeing founder effect with the pattern of spread in South Africa. A founder effect is one where a selection of initial genetic patterns dominate in the cases we get to see – not necessarily because the virus itself is more transmissible (it may be), but because we are selectively learning about the infection from a subset of people who are infected with this particular strain.
“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. The effective reproduction number (which measures the potential for COVID-19 to spread) is likely to be higher than that of Delta. That then will have the undesirable effect of fast transmission.”
What is the risk of spread to NZ?
“Under the current border control we have in NZ, the risk of community transmission with this virus remains low now. However, this may change when the international border restrictions are made less strict in NZ. As such, there is a case to keep the border restrictions in place until we have more information about this strain.”
No conflict of interest.
Professor Miguel Quiñones-Mateu, Webster Family Chair in Viral Pathogenesis, University of Otago, comments:
“What started as yet another variant, it definitely made enough noise for the EU and USA to isolate again a bunch of South African countries.
“Is this the one we all have been afraid of? That is, a highly transmissible, vaccine escape, more virulent variant? Personally, I think it will be difficult for the virus to evolve/select for this trifecta. However, having a canvas of 8 billion people to explore, who knows, it may be just a matter of time.
“We should all be getting vaccinated more or less at the same time, within a logical period of time. This would minimize the opportunity of the virus to evolve, escape from the host immune response and/or vaccine pressure.
“More importantly, I know that in some countries, where access to COVID-19 vaccines is scarce or less-than-optimally planned, people are mixing and matching different vaccines, at times not following the appropriate schemas. Similar to taking antibiotics without prescription or antiviral strategies without the proper guidance, all this could put pressure on the virus, perhaps leading to escape variants.
“The misuse of vaccines and therapies will only accelerate the selection of “something nastier”. Vaccinating as many people, in a relatively short period of time, has to be the goal, and staying away from misusing antiviral treatments. We do have plenty of experience with HIV, HCV, etc, and let’s not start with the overuse of antibiotics.
“Bottom line: get vaccinated and follow the recommendations of your physicians and public health officers.”
No conflict of interest declared.