Why it really matters that the UK Covid strain has already mutated to resemble the Brazil and South Africa strains

Residents in part of Surrey are to be urgently tested for Covid-19 after it emerged the South African strain of the virus may have started spreading in the community. Credit: PA

Tuesday's "hit-it-hard" strategy, of targeting 80,000 people who may have been exposed to the South African Covid-19 variant, is a sign of how we will be living for months and probably years to come.

What I mean is that we have entered an important and troubling new phase of this pandemic, in which new strains that are more resistant to vaccines are being imported and are developing naturally here.

The government's strategy is to take drastic action wherever significant outbreaks of the new imported and indigenous variants occur, with contact tracers knocking on doors and asking people to stay home in a strict quarantine till they have had a test to identify whether they are infected.

So one important initial point is that severe localised lockdowns, of the sort currently being experienced in Tottenham, Maidstone, Walsall and five other areas, are likely to become part of our lives for years.

It means that even after most of us have been vaccinated, the efficiency and efficacy of NHS Test and Trace will be more important than it has been (and of course to date there have been widespread criticisms that it has not been effective enough).

As one senior official told me, Test and Trace's prime function will be "hunting out positive cases as prevalence comes down, sequencing them all and then stamping down hard on any new variant of concern - all to slow down spread [of new variants] to enable vaccines to be adapted".

There is a lot in that statement of importance that needs unpacking and explaining. Here goes.

What matters is that the risk of the new strains being imported from abroad is not the biggest concern of Public Health England and the scientists who advise the government - though they do worry about that.

What troubles them more is the way that this virus has shown that it is already naturally evolving here, such that it becomes more resistant to the current generation of vaccines and acquires the ability to re-infect people who have already had the virus.

To repeat, this evolution of the virus to "escape" the vaccine and natural immunity has already happened - as Public Health England said in a recent paper that almost no one noticed.

PHE, in its "Investigation of Novel SARS-CoV-2 Variant", said: "The spike protein mutation E484K (found in VOC 202012/02 B1.351 and VOC 202101/02 P1) has been detected in 11 B1.1.7 sequences. Preliminary information suggests more than one acquisition event".

To translate, gene sequencing by PHE has identified that the Kent strain of the virus, the one that has been running rife through the UK, has already naturally mutated so that it more closely resembles the Manaus strain from Brazil and the South African strain.

And the point about these strains is that, although they are probably not more deadly than the Kent and original strains, there are concerns that the existing vaccines may be less effective against them (though not totally ineffective).

Here is how one scientist put it to me: "The E484K mutation is the one that has been associated with evading the immune response. It is the mutation in both the Manaus and SA strains (along with the 501Y mutation that we have)".

The PHE document does not say how many instances of this further mutation of the Kent strain have been identified. But a government adviser disclosed this to me:

"They have reported on 11 instances. Some of these are linked, that is the virus has mutated to acquire this E484K mutation, and then spread. However, they are not all linked, so it looks like separately, elsewhere in the country, the virus has also acquired this E484K mutation".

Which implies, since this research is already days old, that this naturally occurring Brazilian/SA strain may already be more widespread than we know.

None of this is a reason to be fatalistic that there is nothing we can do to control this virus and get back to life that feels more normal (though probably not what we used to think of as normal).

But it is an argument for bearing down as hard as possible now on the spread and not releasing lockdown prematurely. For what it's worth, most of Boris Johnson's scientific advisers are by no means confident that his hope of allowing children to return to school on 8 March will be appropriate.

And as SAGE member Prof Colin Semple tweeted, it really matters that vaccinations happen as speedily as possible, to at least suppress the variants that are amenable to suppression.

But there is a subtle and terrible paradox to this virus that we all need to understand, because it will condition the important debate we haven't yet had, namely how we should live once we are through this latest awful phase of the pandemic.

This is how a scientist explained the Covid-19 paradox to me:

"The issue with the SA strain and the UK strains that acquire the same mutation is that they can evade pre-existing immunity to some extent. At present only about 20% of us have previously been infected by the virus (though this is about 30-35% in London). Add to that perhaps another 10% or so from the vaccine (which is rapidly increasing), and we are starting to get to a point where an appreciable fraction of the population will have some evidence of immunity.

"It is at that point that the SA strain and UK strains with the same mutation will start to get a significant advantage.

"When we lift lockdown these strains (and all the others) will be let loose. When we do this, due to the increasing levels of immunity, we will have tipped the balance in favour of these new "escape" (i.e. escaping the immune response) variants. That is what I think will happen. We will lift, and then have the next wave, which will be one of these variants".

So for the avoidance of doubt, by vaccinating the population, and with immunity being created in those who've had the virus, we are creating the very conditions that encourage the virus to mutate, to change, because if it doesn't change it dies. And almost as a matter of logic, these mutations will displace the Kent mutation when it is under control.

What that means is NOT that we can't defeat Covid-19. But it does mean we have to be utterly (possibly eternally) vigilant in identifying where the new strains are occurring, with comprehensive testing and gene sequencing, and then crushing the outbreaks through extreme local lockdowns.

Which is why, as I said, a return to a "normal" way of life is out of the question.