COVID-19: Pseudovirus testing and infection studies – why it takes a long time to find out how dangerous Omicron is

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COVID-19: Pseudovirus testing and infection studies – why it takes a long time to find out how dangerous Omicron is


When it comes to questions about the Omicron variant, scientists are starting to look a bit like parents on a long road trip.

Is it more contagious? More deadly? Could he bypass our vaccine defenses? The most precise answer they seem to be able to give is “it’s too early to tell” or “we just don’t know yet”.

At the heart of all this uncertainty is the fact that knowing the genetics of a virus (which we are doing for Omicron) can be a terrible guide to how it might behave in the real world.

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How transmissible is Omicron?

No doubt that compared to the previous one COVID strains Omicron is seriously impaired. His array of fifty mutations, including 30 in the spike protein, has been compared to entering an “evolutionary gym”.

The virus appears to have had time to build its genome, not only accumulating one type of potentially beneficial mutation seen in other variants before, but acquiring many different versions of each.

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This is the reason for the concern. And the fact that he seems to be increasing in numbers in South Africa, which means he’s not just a genetic bodybuilder. It has the ability to spread.

But to extend how far? And with what aggressiveness?

If we need to reinstate restrictions or make new vaccines against Omicron, we don’t have the luxury of sitting down and watching him prove (or not) his pandemic prowess.

This is where laboratory experiments come in. Scientists need to perform some key tests.

First, check the antibodies of people who have been vaccinated or previously infected against Omicron. This should answer the question of whether it will bypass our immune defenses, and if so, by how much.

Other experiments may test the ability of the virus to infect cells in a test tube – an important clue to whether it is more infectious than the Delta strain – and therefore be able to cause a wave of infections even in small areas. places like the UK where Delta is at high standards.

Are we nearly there yet? Well, it’s frustrating, to do these experiments you have to grow the live Omicron virus in the lab. And even though it was first identified almost three weeks ago, scientists still haven’t produced enough stocks of the bug to begin experiments.

One shortcut is to produce a “pseudovirus” – a harmless chassis borrowed from another virus into which Omicron’s genes are then copied and pasted.

This is the approach that vaccine companies like Moderna, Pfizer and Novavax take to test their vaccines against him, while waiting for a live virus or actual evidence of infections in people who have received their vaccine.

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The jabs will be “less effective”

These approaches worked before. When the worrisome beta variant, which emerged last winter (then known as the South African variant), pseudovirus testing quickly showed a six-fold reduction in the potency of Moderna vaccine antibodies.

Pfizer studied infections of the South African strain in the Israeli population and found that more than 5% of infections in vaccinated people were due to the beta variant, compared to less than 1% in unvaccinated people – a clear sign that the virus passed the vaccine.

And a trial of the AstraZeneca vaccine that was going on in South Africa at the time Beta emerged showed that it was perhaps only 10% effective in preventing mild to moderate COVID, compared to over 60% of effectiveness against the original strain.

These results naturally terrified people about the potential impact of the Beta strain. Widespread surge testing in the UK last spring attempted to contain the variant. Just as we are now starting to contain Omicron.

And consider this. Where Beta had three mutations in the key bit of the spike protein that binds to cells, Omicron has 10.

But in the end, despite his advantage over vaccines, Beta was no match for Delta. Delta has become dominant and the variant has all but disappeared, even in South Africa.

Omicron’s lab tests in the coming weeks could give us clues about its capabilities. Will it be as contagious as Delta, and will it have the ability to bypass vaccines?

Or will it be beta again? If it’s the former, we might have a crucial head start in making improved vaccines that might be our only defense against it.

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But the best clues will come from the variant’s first forays into South Africa and other countries with higher vaccination rates.

The challenge for scientists is to get this information and act on it before Omicron has a chance to spread widely.

Yes, and it still is, this is what he is capable of.

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