Here We Go Again…

Matt Hancock raised the alarm in Parliament yesterday when he said a new variant of Coronavirus was doing the rounds and linked this to the rise in community infections in Kent and London. The press release from Public Health England has the details.

The strain was identified due to Public Health England’s proactive and enhanced monitoring following the increase in cases seen in Kent and London. The variant has been named ‘VUI – 202012/01’ (the first Variant Under Investigation in December 2020).

As of December 13th, 1,108 cases with this variant have been identified, predominantly in the South and East of England. PHE is working with partners to investigate and plans to share its findings over the next two weeks. There is currently no evidence to suggest that the strain has any impact on disease severity, antibody response or vaccine efficacy.

High numbers of cases of the variant virus have been observed in some areas where there is also a high incidence of COVID-19. It is not yet known whether the variant is responsible for these increased numbers of cases. PHE will monitor the impact of this in the coming days and weeks.

It is not uncommon for viruses to undergo mutations; seasonal influenza mutates every year. Variants of SARS-CoV-2 have been observed in other countries, such as Spain.

This variant includes a mutation in the ‘spike’ protein. Changes in this part of the spike protein may result in the virus becoming more infectious and spreading more easily between people.

paper in Nature by François Balloux among others provides some helpful context. He pointed out that he and his team had identified 12,000 variants/mutations, none of which increased transmission or led to more severe infections. Here’s the abstract:

COVID-19 is caused by the coronavirus SARS-CoV-2, which jumped into the human population in late 2019 from a currently uncharacterised animal reservoir. Due to this recent association with humans, SARS-CoV-2 may not yet be fully adapted to its human host. This has led to speculations that SARS-CoV-2 may be evolving towards higher transmissibility. The most plausible mutations under putative natural selection are those which have emerged repeatedly and independently (homoplasies). Here, we formally test whether any homoplasies observed in SARS-CoV-2 to date are significantly associated with increased viral transmission. We do not identify a single recurrent mutation in this set convincingly associated with increased viral transmission. Instead, recurrent mutations currently in circulation appear to be evolutionary neutral and primarily induced by the human immune system via RNA editing, rather than being signatures of adaptation. At this stage we find no evidence for significantly more transmissible lineages of SARS-CoV-2 due to recurrent mutations.

At the Number 10 press briefing that followed Matt Hancock’s announcement, Chris Whitty played down potential fears concerning the new variant, as Ross Clark reports in the Spectator:

Mutations are only to be expected, he said, and many have already emerged. It isn’t clear, he added, whether the new variant is more transmissible than previous ones… There is no evidence, he said, that the new variant is more dangerous to humans than previous versions, and no reason to suspect that this would be the case… Nor, said Whitty, is there any reason to imagine that the new variant will be any more resistant to the Pfizer vaccine or any other vaccine, too few people have yet been given the vaccine for the virus to start developing its own immunity to the vaccine.

The sudden appearance of a variant/mutation – LonKent-20? – along with the rising numbers of reported cases has led to speculation about whether we’ll still give five days off over Christmas. Whitty reminded us that “the fact that some relaxations are being made not to the tiering but to people’s ability to meet their families over Christmas does not mean that they should go to the top of the licence of that. The point of this is, under certain circumstances, for families who wish to, to get together, but they really have to be very very careful”. Hancock said:

On the modelling around Christmas, it all depends on people’s behaviour and the most important thing is that people are cautious and careful ahead of Christmas and during Christmas and hence why we’re saying that so clearly.

Back to Ross Clark in the Spectator:

Should we worry about the emergence of a new variant of SARS-CoV-2, the virus which causes COVID-19? As I wrote in May, the SARS-CoV-2 virus has already mutated once into a form that might be more transmissible. This could possibly explain why Europe and North America have found it harder to contain the virus than have Asian countries. Were we fighting a slightly different disease to the one which emerged in Wuhan in January?

In a recent survey of 46,723 people with COVID-19 from 99 countries, researchers identified more than 12,700 mutations. “None of these mutations are making COVID-19 spread more rapidly,” according to Lucy van Dorp, a professor at University College London’s Genetics Institute and one of the co-lead researchers on the study.

But what today’s news has done, in particular the decision to shift the capital into a higher tier, is to change the mood. From a picture of declining infections in late November and early December, we are heading back, once more, into a period of tighter restrictions.

Once again, as throughout this crisis, questions at this evening’s briefing focused on whether tighter lockdowns would be imposed. This time, there were also repeated questions on whether the relaxation of rules on households mixing over Christmas ought now to be revisited. Given that Germany and other countries have started imposing lockdowns across Christmas, I give it until about Thursday until Boris is back at the lectern announcing that, regrettably, it is going to be necessary to cancel Granny’s visit.

Ross Clark’s piece is worth reading in full.