What we know about Omicron variant so far


The first fatality due to an Omicron infection has been confirmed from the UK, the variant has now reached China – where the Sars-CoV-2 was first found – and several countries are pressing on with large booster dose campaigns to blunt the threat from the heavily mutated virus.

In the short time since it was designated as a variant of concern (VOC) at the end of November, Omicron is confirmed to have two of the three most threatening traits a mutated Sars-CoV-2 can pick up: it is more transmissible and resistant than any configuration of the coronavirus that causes Covid-19.

The severity of the disease it leads to – the third characteristic being watched for – is yet to be confirmed, although anecdotally, it could be less severe.

Several scientists see the arrival of Omicron as consistent with a prediction that the coronavirus will eventually become endemic, evolving every now and then to lead to some serious outbreaks, like what was seen in the annual flu outbreak in 2014-15.

Two evolutionary biologists, University of Cape Town’s assistant professor Darren Martin and Temple University professor Sergei Pond, in a recent online discussion sketched out what they believe will be the main scenarios for Omicron’s evolution, building on what has been seen so far with the Sars-Cov-2.

The assessments consider the immune or selection pressure the virus faced and is likely to face – this is the nature of collective immunity that can dictate the evolutionary landscape of a contagious pathogen, which naturally attempts to evolve to keep spreading.

Scenario 1: No immune pressure

In this case, Omicron spreads with no selective pressure like the first version of the virus during the early phase of the pandemic. But such a situation is unlikely, since now many people worldwide have either been infected or vaccinated.In such a situation, Omicron is unlikely to “coast” across the global population like the virus that spread out of Wuhan did until December 2020 (when Alpha variant began taking over).

Scenario 2: Weak or moderate pressure

What happens when Omicron faces a weak or moderate selective pressure? The scientists estimate the virus will become the dominant strain, and evolve rather slowly without significant changes in how it inherently spreads, resists antibodies, and causes disease. Over time, some mutations may better these functions, but probably only in small pockets.

Scenario 3: Strong selective pressure

Several factors can strongly force Omicron to mutate, including competition with the fittest Delta sub-lineage; low genetic barriers that allow it to pick up certain mutations; and, if Omicron evolves with an alternative animal species, it could select additional mutations to better infect humans. This scenario is one to watch out for since it would “be expected to play out over a considerably shorter time frame”.

Scenario 4: Recombination wildcard

Recombination is when a concurrent infection with two different variants can cause the virus to take an evolutionary leap after the fittest of mutations from both make through.

There are already two distinct Omicron lineages, and more may be discovered over time, which could recombine, the authors suggest. The increased infectivity of Delta and Omicron too “substantially increases the probability of mixed infections”, which could lead to such recombination.

This scenario sounds grim but presently, the scientific community has “no idea whether the potential even exists” and what might happen if such a thing does indeed happen.

Predicting Omicron’s evolution is difficult – Pond and Martin titled their arguments as a “Fool’s Errand” — and only time will tell the route the virus takes, but the scenarios will help shape how sequences of the virus are analysed and, in the future, as more data emerges, predict which of the cases are likely to become reality

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