The emergence of yet another virus variant of concern causing COVID is a wake-up call for those of us who are remaining vaccine hesitant or opposed to vaccination. Herd immunity will ultimately shield us from variants penetrating our communities.

Although laboratory tests are limited they are predictive of both levels and types of antibody responses in humans. Antibodies can be assessed in microneutralisation assays in the laboratory for effectiveness against omicron. We should know these results from scientists around the world over the next few days.

However, we really need a variant proof vaccine that can protect us from different virus mutants of SARS-CoV2 and stimulate immunity with the production of broadly neutralising antibodies.

Coronaviruses share some regions of the spike protein (S2) that don’t mutate as much as the hypervariable S1 region, which has the receptor binding domain. Therefore, broadly neutralising antibodies made to the S2 region can block virus fusion to our cell membranes, preventing entry and thus replication of virus variants.  

A variant that causes less severe disease but is more transmissible from human to human would overtake Delta as the new dominant strain in circulation. However, other variants will continue to pop up amongst subpopulations of the unvaccinated and also in those who are immunosuppressed or immunocompromised with co-infections. It is vital that vaccination campaigns build momentum especially in places like Sub-Saharan Africa, where HIV and Hepatitis C are also widely prevalent.

On Boosters:

​"Theoretically, a booster aimed at the spike protein will allow the immune response to ramp up with memory B cells producing neutralising antibodies. However, with a highly mutated variant in the S1 region of the spike, the common regions of the S2, between the original vaccine strain and the new variant of concern (VOC) omicron, will induce a broadly reactive immune response. Therefore, having any booster that sustains our protective antibody levels is wise at this stage.

The occurrence of a new and potentially disruptive variant has always been expected when the virus remains unchecked in millions of people. It will continue to mutate and that is why we need to remain vigilant and agile in our responses. This variant almost certainly emerged in an immunocompromised individual who could not clear the original infection. Most likely an unvaccinated HIV patient in South Africa where the virus can replicate and evolve.

Vaccinating more Africans (and people in developing countries in general) would help long term to try and reduce this reservoir of infection, but is not a quick fix. At some stage, the virus will mutate so much that it will be a strain not a variant and then we will have to call it SARS COV-3 - once this happens we would expect new biological properties to emerge of biomedical significance. We are not there yet but unfortunately, we are well on the way.

New modelling will almost certainly be needed when we have new information on infectivity, incubation periods etc. This will be population dependent and will take weeks to gather. This variant only got its name a week or so ago and yet it is already in 12 countries so we can assume that it is highly infectious. It also has more mutations than any variant seen so far that combine infectivity and the possibility of vaccine evasion. All good reasons for caution.

If Omicron ends up being more infectious, but less severe in all age groups, vulnerable populations and vaccinated populations, then that wouldn't necessarily be a bad situation. It may not affect how well-vaccinated countries continue to open up. Of course, the risk again is that if it takes hold in unvaccinated regions around the world and generates lots of infections, including in immunosuppressed people in whom the virus can replicate for longer, then that would be a risk for a new, more dangerous variant to appear.

Boosters can improve immunity by increasing levels of certain types of antibodies that stop the virus from infecting a cell, so-called "neutralising antibodies". Data from Israel has shown the booster doses have had an impact on Delta there. So it is likely that a booster would improve immunity against Omicron; however, there are unknowns, such as by what degree a booster would protect against mild or severe disease.

Can lab tests tell us if the vaccines will work against Omicron? Or are the only accurate tests those which assess efficacy in infected humans?

There are different qualitative or quantitative tests where stored serum from vaccinated people can be tested against the virus to see how strong the neutralising antibody responses are. While it's not the same as seeing how vaccinated people respond to the variant in real life, it can give some idea if the vaccine will have some effect against Omicron.

​If this variant enters the community, will there be more lockdowns?

If Omicron is more infectious and displaces Delta, causes as much or more severe disease, and renders the vaccines ineffective, then yes, lockdowns may be back. But that's in a "perfect storm". If the vaccines prove effective, and Omicron causes mild disease despite being more infectious than Delta, then the chance of lockdowns are much less likely in a highly vaccinated country.

The vaccines work by stimulating the immune system through exposure to a replicant of the viral spike protein. This immunity has been demonstrated to be strong against emerging variants to date. It is expected that the current vaccines will continue to provide immunity against the Omicron variant – the question is how strong this may be, which is unknown at this time.

It is possible to test the new variants against neutralising antibodies in the lab. This was done when the Delta variant emerged. These studies give an indication that the generated antibodies work against the virus, but we do require field experience before understanding the effectiveness of the vaccines.

The emergence of a new variant, though unsettling, is far from unexpected. Viruses constantly mutate and take on new forms, and the level of existing immunity against a new variant is key in determining the impact an emerging strain will have. Scientists will now need to quickly use established laboratory methods to determine how much immunity blood from vaccinated people has against Omicron and we will then be able to use the established relationship between immunity and vaccine efficacy* to predict how existing vaccines will perform against Omicron, and therefore how much impact this new variant may have on the inroads we have made in the fight against COVID-19 disease. Closing borders may buy us some time to gather the data to answer these questions, however, as we have seen previously, with both the original strain and with Delta, a virus will ultimately find its way past these barriers, and it will come down to how effective the immunity we have generated to date is against the new variant.

Primarily what will be important for Australians in the short term is how well existing vaccines work against the new variant. If our vaccines are still able to protect against severe disease resulting from Omicron infection then we will be well placed from a public health perspective. In the longer term, and from a global health point of view, a more mild variant would be a positive for countries with low levels of vaccination and immunity.

Booster shots increase immunity against the virus. What we have seen is that higher levels of immunity are required to combat new variants (both to protect against any infection and severe disease). Therefore, boosting immunity overall will help in combating disease from emerging variants.

* Khoury, Cromer et. al. Nature Medicine (2021) and Cromer, Steain et. al. Lancet Microbe (2021)

We do not have enough data to determine vaccine effectiveness against Omicron or disease severity, so any claims about either at this stage are not evidence-based.  The pathogen genomics show mutations that are associated with resistance to neutralising antibodies and immune evasion, suggesting some degree of vaccine escape is likely.  Vaccines will still likely provide protection against severe disease, but we do not yet have data to quantify this.

For Australia, speeding up high 3rd dose coverage is important, because waning immunity after dose 2 starts 2-3 months after the second dose – the booster can be given any time from 2-6 months after the second dose, and we should be encouraging rapid, high 3rd dose uptake. We should also be ensuring supply of the paediatric vaccine formulations and a recommendation for kids 5-11 years asap.  And we should be talking to companies and making procurement plans for Omicron-matched boosters as well as the two new promising antivirals.

The global issue of concern we have had for most of this year has been the sharing of IP rights and vaccine ingredients for vaccine manufacture by developing countries that can manufacture vaccines – India, South Africa, Brazil, Taiwan & Cuba. This has impacted the production of and comprised distribution of vaccines. Vaccine Equity is another major issue with most of Africa having very poor vaccination rates. This factor has impacted and will impact the emergence of new variants of interest and concern.  We have a moral and ethical imperative to work towards vaccine equity.

This new variant descends from the B.1.1 lineage and is 'unprecedented' and 'very unusual' in the number of its mutations. B.1.1529 has 32 mutations located in its spike protein. These include E484A, K417N and N440K, which are associated with helping the virus to escape detection from antibodies. Another mutation, N501Y, appears to increase the ability of the virus to gain entry to our cells, making it more transmissible. Another important matter to note is that most of the major mutations are located at the receptor-binding domain of the spike protein, the exact location where antibodies from vaccines are binding/targeted. In other words, the 32 mutations detected in the new variant’s spike protein will change the shape of this structure, making it problematic for the immune response induced by the vaccines. These mutations can make the spike protein less recognisable to our antibodies. As a result, they won’t be as effective at neutralising the virus, which is then able to slip past immune defences and cause infection.

While the 32 mutations in the spike proteins is a 'real concern', giving this variant a better way to evade antibodies from vaccines, this should not deter the current worldwide vaccination drive including booster doses together with the 'weapons' that we already have. We should not forget that already we have the ‘weapons’ (e.g., masks, social distancing, proper hand hygiene etc.) to reduce the risk of becoming infected. It should therefore be our main goal to slow down virus spread by adhering to the existing hygiene and speeding up the vaccination including the booster doses process (especially in vulnerable populations). Getting vaccinated against COVID-19 is the strongest form of protection.

Every time the virus reproduces inside someone who is not vaccinated, there’s a chance of it mutating and a new variant emerging. This is a numbers game. It’s a random process, a bit like rolling dice. The more you roll, the greater the chance of new variants appearing. It’s basically a ticking timebomb. The main way to stop variants is EQUAL global vaccination. The emergence of Omicron reminds us of how important that goal remains. We must get vaccines to these people as quickly as possible (especially in countries that are behind in vaccination rate), both to help the people there who are vulnerable but also to stop new variants from emerging.

Let us not forget that in South Africa, where just 35 per cent of people are fully vaccinated, the variant has begun to spread rapidly. A number of factors could be contributing to the rising caseload, including the nation’s low vaccination rate.

Vaccine equity is a global problem! If we don’t address this quickly enough, our exit from the pandemic will be set back, possibly for months or years on end. The only way is to sprint towards the finish line to have any protection against these emerging variants. In the case of the Omicron variant, as explained before, it contains the recipe for disaster as an initial look at the viral genome suggests the possibility of immune evading capabilities is higher compared to other variants of concern. As we are currently looking in-depth at its pathogenicity, virulence and transmission, we will only get a clearer picture in the coming weeks. But countries cannot rest on their laurels and risk another variant wreaking havoc similar to what Delta is doing currently.

One of the biggest hurdles in getting vaccines in time all over the world is the logistics/transport involved. Another issue that proved to be a stumbling block in ensuring vaccines reach countries in time was “vaccine hoarding” by vaccine producing countries and rich countries to ensure the majority of doses reached their own population first. If countries are able to produce vaccines/vaccine technology 'in-house' it will enable these vaccines to reach their populations much faster which is vital in providing protection and stopping newer variants from emerging.

China is one good example. All of their vaccines are produced in-house and they were one of the first to control the pandemic. The emergence of newer variants from China is almost non-existent as they were able to vaccinate the majority of their population at breath-taking speed.

It is reassuring to see that World leaders are acting fast to curb transmission of the new variant of SARS-CoV-2 named Omicron. But we must remember this is not the last mutation, viruses mutate all the time as this is an inherent property of all viruses. However, not all mutations are lethal, it's very early on to comment on the Omicron variant. We need to wait at least another 2-3 weeks to see data from other countries where Omicron has spread to, to understand the virulence, infectiousness and capacity of the variant to evade the immune response across different populations.

We know that selective border closures don’t work, the virus doesn’t understand borders. It's very likely what we are seeing with Omicron is just the tip of the iceberg and it has probably spread to many more countries than we currently know of.

New variants will continue to emerge but we can only live with an endemic level of transmission of SARS-CoV-2 when we have reached a very high level of vaccine coverage in the general population across the world. We need to put all our efforts into ensuring global vaccine equity specifically for people in low middle income countries where less than 10 per cent of the population has been vaccinated.