It’s a sign of the times that the meaning of a single Greek letter is immediately understood and can strike a frenzy in the media and dread in the public. Omicron is the latest “variant of concern” according to the World Health Organization (WHO). Just two months ago I wrote here about variants of interest and variants of concern, warning that the recent delta variants of SARS-CoV-2, responsible for a massive wave of COVID infections over the summer, was likely not the last significant variant of this pandemic. On cue the omicron variant arrives to threaten our Winter.

While it is definitely a cause for concern, it is still too early to conclude that omicron will be another delta variant or worse. Here is what we know so far.

First, to quickly review, variants of the SARS-CoV-2 virus are caused by mutations in its genome. This is not a particularly fast mutating virus (not as fast as flu viruses, for example) but the number of infections around the world provides ample opportunities for mutations to occur. Most mutations are silent, meaning that they do not change the amino acid sequence of the protein for which they code. Such mutations, however, may influence expression, although this may not be relevant in a virus. Many of the mutations which do alter which amino acids are coded for may still not produce a functional change in the protein – it will still fold the same way and act the same way. A small subset of mutations are functional, in that they alter the structure and function of the protein they code for. Many of these mutations are lateral moves, not dramatically altering the behavior of the overall virus. But some mutations do alter the virus’s behavior in a clinically significant way, and these are the mutations that scientists are interested in.

With the coronaviruses, the primary protein that represents the “business end” of the virus is the spike protein. This sticks out from the outer shell of the virus like a crown, giving this family of viruses its name, and is also responsible for its ability to infect host cells. Mutations in the spike protein are of particular interest.

The WHO has been tracking the emergence of new variants of the SARS-CoV-2 virus throughout the pandemic. It has created a list of variants of interest, which have identified mutations that might alter the characteristics of the virus. These mutations are likely to make the virus either more infectious, more deadly, or allow it to escape detection or preventive measures (like masks, distancing, or vaccines). In addition, to be a variant of interest the variant must be responsible for significant community transmission. If a variant is not spreading, it’s not a threat.

One notch up in the threat level is a variant of concern, which the new omicron variant has been designated. These are variants of interest that also have demonstrated:

Increase in transmissibility or detrimental change in COVID-19 epidemiology; OR
Increase in virulence or change in clinical disease presentation; OR
Decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics.

Omicron was first detected in South Africa. We need to recognize that South Africa has a robust detection system, sequencing the entire genome of viruses taken from COVID patients in order to monitor for the emergence of new variants. Our preliminary data on omicron comes mostly from them. Right now the delta variant is the variant to beat, and I mean that literally. It is responsible for almost all COVID infections around the world, outcompeting all other variants. Any new variant must therefore outcompete delta in some way to get a foothold.

Recently a variant of interest, mu, was identified that had a relative degree of resistance to existing vaccines. However, it was not able to outcompete delta, and so essentially fizzled. This is often what happens during a pandemic. Evolutionary selective pressures favor viruses that spread more easily and aggressively, so these variants dominate over time. These are not necessarily the same properties that allow a virus to be more deadly or escape treatments. There is therefore a statistical probability that as a pandemic simmers along, variants predominate that produce milder disease. This is one way pandemics peter out. So far we have not been so lucky with COVID-19.

The question now is – will omicron go the way of mu, not able to compete against the delta variant, or will it replace delta and cause new waves of infection around the world? At this point either outcome is possible. The WHO is concerned because in South Africa where the variant is being detected there has been a spike in infections. If this is due to the variant itself, we need to prepare ourselves for a new wave of the pandemic. However, the WHO has not ruled out that other factors may be responsible for this increase in infections. This is scientists being cautious, and we need to be patient and let them do their investigations.

Omicron is also concerning because it has 30 mutations (26 of which are unique to omicron) on the spike protein itself. This is more than any other variant. This means the omicron variant has the potential for many new properties all together.

Regarding disease severity the WHO reports:

Preliminary data suggests that there are increasing rates of hospitalization in South Africa, but this may be due to increasing overall numbers of people becoming infected, rather than a result of specific infection with Omicron. There is currently no information to suggest that symptoms associated with Omicron are different from those from other variants.

It will likely take several weeks of gathering data before we can make a firm conclusion about disease severity with omicron. In terms of the effectiveness of existing countermeasures, there is early reason for concern in that the reinfection rate seems to be higher with omicron. Therefore, antibodies from past infections may not be as protective against this variant. But again, this needs to be confirmed. The effectiveness of existing vaccines (a huge question) is being actively investigated, and we should have some preliminary data in a few weeks. The first studies are looking at the effectiveness of antibodies from vaccinated individuals at neutralizing the omicron variant. It will take longer to gather epidemiological data on how the variant is behaving out there in the world.

Existing testing is still effective at detecting this variant, and in fact the PCR test can not only detect it but identify it as the omicron variant. This will make it easy to track the spread of this variant.

Again, it is too early to tell what the full implications of the omicron variant will be, and it is good that scientists are jumping on this variant to learn as much as possible as quickly as possible. Best case scenario, we will have a mu-variant fizzle. The worst case scenario is that we are in for another wave of the pandemic to sweep the world. At this time the full spectrum is possible, but we will know more in a matter of weeks.

Regardless, the omicron variant has implications for public policy. First, we need to recognize the success of the South African monitoring program and replicate it in as many countries as possible. Their early-warning system has given us a jump on this variant. These systems also need to be coordinated world wide, with free sharing of data, so that anywhere a new variant emerges we will learn about it quickly.

Omicron and other variants, like delta, have implications for our vaccination program. These newer variants of concern are tending to drift away from the original type virus against which the vaccines are targeted. While the vaccines are still effective, efficacy is tending to decrease with these newer variants. This absolutely does not decrease the need to get vaccinated – it increases it. We now know that the booster shots are significantly increasing antibody titers, above that of simply being fully vaccinated. These increased antibodies will be effective even against variants that are partially resistant. Right now boosting is the best defense against new variants.

Meanwhile vaccine manufacturers are exploring updates to their vaccines to cover emerging variants, but do not wait to get vaccinated or boosted. The current vaccines are your best protection against delta and omicron.

The emergence of variants also shows that a variant can emerge anywhere in the world and still spread to anywhere else in the world. This means we have to seriously consider our global vaccination strategy. Essentially we need to increase our efforts to vaccinate the world. A rich country with high vaccination rates can still be threatened by a variant that emerges in a poor country half-way around the world.

Vaccines also reduce the chance of new variants emerging. Prolonged infection where the virus has a chance to replicate extensively within a single host is where mutations tend to emerge. Vaccines reduce the duration of disease and the ability of the virus to replicate, dramatically decreasing the opportunity for new mutations to accumulate.

The year 2020 of the COVID-19 pandemic was defined by a race to slow down spread of the virus to give scientists time to develop effective vaccines. We essentially failed to contain the virus, but scientists did succeed in developing multiple highly effective vaccines.

The year 2021 of the pandemic is defined by a race to get the world vaccinated before new variants emerged. We lost this race, partly because we did not get enough vaccine distributed in poorer countries, but also due to vaccine resistance in wealthy countries. We have likely now missed our window to prevent SARS-CoV-2 from becoming endemic, meaning an enduring part of our world.

But the race is not over. These newer variants, such as delta and possibly omicron, have extended the pandemic. But they did not hit the full reset button on the pandemic, because the existing vaccines are still effective. Perhaps 2022 will be defined by the next leg of the race – can we get enough of the world vaccinated before a truly scary variant emerges, one that can mostly or completely evade the vaccine, or that is much more deadly than existing variants?

This is an open question. One thing is for sure – this pandemic is not over yet. While we are all anxious for things to get back to normal, they are not normal. They may never return to pre-pandemic normal. We now have to live with this virus, and that means doing whatever it takes to get as many people vaccinated as possible.

Author

  • Founder and currently Executive Editor of Science-Based Medicine Steven Novella, MD is an academic clinical neurologist at the Yale University School of Medicine. He is also the host and producer of the popular weekly science podcast, The Skeptics’ Guide to the Universe, and the author of the NeuroLogicaBlog, a daily blog that covers news and issues in neuroscience, but also general science, scientific skepticism, philosophy of science, critical thinking, and the intersection of science with the media and society. Dr. Novella also has produced two courses with The Great Courses, and published a book on critical thinking - also called The Skeptics Guide to the Universe.

Posted by Steven Novella

Founder and currently Executive Editor of Science-Based Medicine Steven Novella, MD is an academic clinical neurologist at the Yale University School of Medicine. He is also the host and producer of the popular weekly science podcast, The Skeptics’ Guide to the Universe, and the author of the NeuroLogicaBlog, a daily blog that covers news and issues in neuroscience, but also general science, scientific skepticism, philosophy of science, critical thinking, and the intersection of science with the media and society. Dr. Novella also has produced two courses with The Great Courses, and published a book on critical thinking - also called The Skeptics Guide to the Universe.