What is the new UK Covid strain all about and why are scientists worried?

[I am a UK-based infectious disease epidemiologist with specialism in new and emerging infections, and write regular “explainer” posts about the pandemic, of which this is the latest. There’s currently a lot of misinformation and misunderstanding swirling about the internet regarding COVID-19 — so please do remember to check someone’s credentials if they are posting about it. You can find my CV on LinkedIn (Georgia Ladbury). Usual disclaimer that I am writing in a personal capacity and my views don’t necessarily reflect those of my employer]

It’s taken me a while to write about this one because it’s Christmas week and there’s much to do and kids under my feet and also, evidence about the new variant is coming out so thick and fast that as soon as I had time to write something, what I knew was already out of date.

Soooo, here goes, and heavily caveated that whatever I wrote today will likely be old news and potentially inaccurate in a few days’ (hours’?) time! Also expect typos as I’ve had no time to proofread what with the mince pies that need baking etc.

**WHAT IS THE NEW STRAIN AND HOW DID IT ARISE?

Mutation sounds a scary thing, but actually it’s something that viruses do all the time. When they replicate within cells, they must copy their genetic code (RNA), and in doing so they quite often make mistakes — as you would if you were copying out lines from a text, for example — you’d expect to make a few typos. Mutations are basically those typos, and the new lines of “text” are new strains. Many of those mutations make no difference whatsoever to what the viral strain’s RNA ultimately codes for (these are called “synonymous” mutations). Others (non-synonymous mutations or deletions) make a difference in what the virus codes for, but even then, only a subset of these will potentially go on to give a new virus strain a competitive advantage over the others that are in existence.

SARS-CoV2 (the virus that causes Covid) has mutated many times since it arrived on the scene, with thousands of strains in circulation over the course of the pandemic. Mutation is to be expected, particularly in areas of high prevalence where there is a lot of virus about. However, while it’s not unusual to see new strains, this new UK strain everyone is talking about, known as B.1.1.7. , or VUI202012/01 (first Variant Under Investigation in December 2020), or VOC202012/01 (Variant Of Concern) (I know, I know, not exactly names that trip off the tongue, unfortunately) *is* unusual in that it carries so many mutations at once — 23, in fact — although only 17 of these result in changes in what the B.1.1.7. strain codes for (the other six are “synonymous”).

It’s unusual to see so many mutations all at once in one strain. We don’t know for certain how it came about, but the leading hypothesis is that some poor individual was chronically infected with SARS-CoV2 for a long time, their immune system kept trying to eliminate it, and in response, the virus in their body kept ducking and diving from these immune responses, eventually resulting in this strain that has so many mutations. Yep, you read that right: the virus strain that has cancelled Christmas is thought to have originated in *one* person — and if that isn’t a lesson in how we all as individuals can play a role in how this pandemic pans out, then I don’t know what is.

**WHAT MAKES SCIENTISTS THINK B.1.1.7 IS MORE TRANSMISSIBLE?

There is no smoking gun yet that proves beyond reasonable doubt that this new strain is more transmissible, but there is sufficient data that scientists strongly suspect that it is. That evidence comes from various different sources:

(1) Genomic — several of the mutations that the strain carries have been experimentally or epidemiologically associated with potentially causing higher transmission in past strains — and we don’t yet know what effect having all of these mutations in combination might be

(2) Epidemiological — the strain has rapidly a stonking first place in terms of which strains are mostly circulating in London and the South East. While it can be difficult to what degree this is due by a biological difference in the virus’ behaviour, versus how much it could have been precipitated by human behaviour (e.g did the strain get lucky by finding itself at a a few super-spreading events in Kent pubs and get a nice head start on other strains that way?), the fact that the it spread very rapidly in London and the South East even during the lockdown2, despite rates falling elsewhere, together with data that suggest behaviours in this region weren’t markedly different from behaviours seen elsewhere, make the case for the former explanation stronger.

(3) Virological — it seems that the PCR tests for people infected with this strain may have lower “cycle thresholds” (“ct”s) than for those infected with other strains. A lower ct is an indication that you are shedding more virus (because the PCR machine doesn’t need to cycle through as many rounds before it shows up as positive).

So there is a bunch of evidence that means that, if B.1.1.7. were a criminal, you’d definitely arrest it on suspicion of being more transmissible, and remand it in custody without bail while you collect the evidence that would be needed to convict it beyond reasonable doubt. And that is exactly what scientists are doing right now- collecting that evidence, growing the virus in cells and in animal models, looking back closely at the genomic and epidemiological data over the past few weeks to learn more about how this virus has spread and who it has infected, in order that we can understand more the mechanisms and the extent of any increased transmissibility. For now the data are sparse, but they are enough to act, and certainly enough to urge huge caution from the public so that it doesn’t get horribly ahead of us before we understand it better.

*WHAT ARE THE POSSIBLE IMPLICATIONS OF THE NEW STRAIN?

*…on severity?

Evidence is being collected, but to date it looks as though the strain does not cause more severe illness than other strains. You’re more likely to catch it, but as an individual you’d expect the illness it causes to be largely the same.

*…on population spread, hospitalisations and deaths?

Unfortunately, even though we think that the severity is no worse, the fact that we suspect it’s more transmissible would mean faster spread and a concomitant increase in hospitalisations and deaths, simply because more people are likely to catch it. Remember the idea of “flattening the curve” to prevent the healthcare system from being overwhelmed? A more transmissible strain would do the exact OPPOSITE of that, and potentially put a lot of extra pressure on the health system.

There’s a lot of talk about how the strain might be more transmissible in children, but at the moment that is largely speculation and not backed up by hard and fast evidence. Again, scientists are working hard to provide that evidence. Until that exists it’s difficult to say whether the emergence of this strain should change our approach to education provision — although early modelling data released last night do suggest that it may not be possible to bring the pandemic under control under Tier 4 if schools remain open. We will know more over the coming days.

*…on vaccines?

Some of the mutations are in the region of RNA that codes for the spike protein of the virus, which is the bit of the virus that the vaccines have been developed to target. However, the vaccinologists seem quite confident at this stage that these shouldn’t have much of an impact on the vaccines, as they have been made to recognise various bits of the spike protein (it’s a bit like, if I had a different nose supplanted onto my face, you’d still be able to recognise me from my eyes, ears, mouth, hair — every other bit of my face). However, if it turns out that the vaccines do work less effectively against this strain, it’s feasible to tweak them so they suit the new strain better; it would just take a few weeks.

So vaccines are still expected to work at an individual level. However, because spread would be expected to be faster and higher, we would need a higher proportion of the population to be vaccinated and faster before we could effectively ease the pressures on the health service and bring the pandemic under control. So the challenges just stepped up a notch.

*…reinfection?

Again, a bit of an open question. Does the new strain mean that it can evade protection by immune responses in people who have been infected before? This remains to be seen; however, similar to vaccine immunity, the fact that the immune response garners a variety of antibodies targeting the virus, hopefully not. Again, scientists will be working hard to set up surveillance systems and studies to answer that question in coming weeks and months, but as yet there’s no definitive answer.

*…treatment?

Possibly some of the antibody treatments we have developed for severe cases of infection may no longer work. But other ones likely will. Again…we need more evidence before we have hard and fast answers on this one.

*SHEESH! THAT ALL SOUNDS AWFUL! THROW ME A BONE! WHAT’S THE GOOD NEWS???

There are various bits of good news:

(1) We have *really* good genomic surveillance

The sequencing data and surveillance of emerging viral strains that we do in the UK really *is* “world-beating”. COG-UK, the consortium that co-ordinates the surveillance, has contributed to 43% of the dataset of all of the known strains of SARS-CoV2 that circulate in the world — that’s not because we have loads more strains circulating in the UK, it’s because we have really good capacity to detect them. It’s entirely possible that highly transmissible strains are emerging elsewhere in the world, and countries simply don’t know about them because they don’t do the sequencing. So, odd though it seems, it’s a good thing that we’ve picked up this new strain. Knowledge is power. Knowledge leads to understanding which leads to being able to make an informed and targeted response to these developments.

(2) Scientists are working on it!

Precisely because we’ve identified this strain early, scientists are now busy working on all these questions raised above. We will get more evidence, we will get more answers. It’s all in train. It’s just a question of sitting with the uncertainty for a bit and being patient — and goodness knows we’ve all learned how to do that this year.

(3) The control measures you already know about it should work!

Limit your contacts. Hands — face — space. Meet outdoors and if you can’t, ventilate.

There is no known reason why this new variant would be able to evade these measures. My advice to you is, even if you’re not living in Tier 4, act as though you are. Step up your level of vigilance and caution — especially tomorrow if you’re intending to see people from other households. Remember how I said we need to remand B1.1.7. in custody while we gather more evidence? The way to do that is to prevent it from spreading around. And that is up to us.

So to sum up:

Hands — Face — Space — Outdoors/ventilate — Limit your contacts.

And patience.

I’m an infectious disease epidemiologist with special interest in zoonoses, new & emerging infectious, One Health, and interdisciplinary public health research