We’re in a new year and we have also entered a new phase of this pandemic. So I thought I’d start off the new year with a quick catch-up thread on the UK variant B.1.1.7 and where we are at in this pandemic.
The variant caught scientists' attention in early December based on a surge in cases around Kent and sequencing data showing it carried a host of mutations. (I wrote about this and how a quirk in the PCR is helping track it here: sciencemag.org/news/2020/12/m…).
CAVEAT: The pace at which we have learnt about this new variant is astonishing. But it’s important to realize that a lot of crucial lab experiments take longer. Most data now is looking at noisy epidemiological data and making inferences based on that.
Having said that: The picture is becoming clearer.
Good news first: There still is no evidence that the variant causes more severe disease or that it can reinfect people more easily or circumvent vaccine-induced immunity. Still, we need to stay vigilant.
The bad news: The evidence has only become stronger that B.1.1.7 is more transmissible and potentially a lot more transmissible than previously circulating #sarscov2. That has potentially massive consequences for the course of this pandemic.
Evidence comes from this preliminary report from @_nickdavies and others from @LSHTM for instance, showing the variant increasing in frequency across the UK. cmmid.github.io/topics/covid19…
@_nickdavies @LSHTM "The continued rapid spread of VOC 202012/01 in England to high frequencies (50% or greater in all NHS regions as of 29 December 2020) makes it less likely that the spread of this variant is due to a founder effect or an otherwise selectively neutral effect."
@_nickdavies @LSHTM Recent report by Imperial College makes the same point:
"While rapid growth of the variant was first observed in the South East, similar growth patterns are observed later in London, East of England, and now more generally across England.”
@_nickdavies @LSHTM Additional data from Denmark (which like UK is doing a lot of sequencing), suggests they are observing a similar pattern of the new variant spreading fast locally.
@_nickdavies @LSHTM While the evidence is convincing that B.1.1.7 is spreading faster there are still a lot of question marks about how much faster. Given the data it’s hard to disentangle the effect of the variant spreading faster and changes in behaviour etc.
@_nickdavies @LSHTM Imperial report estimates what the variant adds to the R of #SARSCoV2 in a number of different ways. As you can see, best estimates range from 0.36 to 0.68. That would mean, on average, every person infected with B.1.1.7 infects an extra 0.36 to 0.68 persons compared to earlier
@_nickdavies @LSHTM Even if the truth turns out to be close to the lower estimates or please, please, please, below that, it is still a big effect. And remember: This is exponential growth, so the effect over time becomes massive.
I don’t think it has really sunk in, how serious this is.
@_nickdavies @LSHTM What does this mean for the pandemic?
Many countries have managed to reduce infections to low numbers by layering a lot of public health interventions on top of each other: teleworking, physical distancing, masks, no large gatherings, some kinds of shutdown etc.
@_nickdavies @LSHTM The idea was that if you do these things well enough, you get the effective reproduction number Rt below 1, so every infected person on average infects less than one other person. That means the virus does not spread and there is some wiggle room to keep schools open for instance
@_nickdavies @LSHTM That wiggle room has just become substantially smaller. If estimates are roughly right, keeping schools open is probably not possible.
Or, if you think of it in terms of the Swiss cheese model, we can afford fewer, smaller holes in the cheese.
@_nickdavies @LSHTM We have entered a new phase of this pandemic. On the one hand vaccinations have started, on the other hand this new variant is spreading faster, potentially causing a lot more sickness and death in a short time. Also: more people will need to be immunised to reach herd immunity.
@_nickdavies @LSHTM It’s not what anyone wants to hear, but the coming months may well be the hardest of this pandemic. If you’ve been thinking of vaccines as the light at the end of the tunnel: Yes, that light is there, as bright as ever. But the tunnel just got a bit darker and a little bit longer
@_nickdavies @LSHTM One addition: This is not the time to throw up your hands in despair and give up. Quite the opposite. We know what we need to do. We just need to do it better. This is the time to draw on whatever strength we have left and redouble our efforts to stem the spread of this virus.
@_nickdavies @LSHTM People love to say how this or that measure is "just postponing” things. Well, with vaccinations underway, “just postponing” things is exactly what we need to do. The variant is probably in many, many countries, but it is still early days and slowing it down will save lives.

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More from @kakape

29 Dec 20
"Although there is no information that infections with these strains are more severe, due to increased transmissibility the impact of #COVID19 disease in terms of hospitalisations and deaths is assessed as high."

@ECDC_EU risk assessment of new variants:
@ECDC_EU "The probability of increased circulation of any SARS-CoV-2 strains and this placing greater pressure on health systems in the coming weeks is considered to be high due to the festive season and, higher still, in countries where the new variants are established."
@ECDC_EU "The UK has demonstrated that their sequencing programme is able to detect emerging variants. Ideally, Member States should aim for a similar timeliness and fraction of samples sequenced, although this will depend on the availability of resources."
Read 5 tweets
29 Dec 20
Finally read the new update on UK variant B.1.1.7, posted yesterday, which includes a study suggesting the variant is no more (or less) severe than prior virus variants.
Just a very brief thread (or read the entire document here:
Researchers took 1769 cases of people infected with the new variant and then looked for 1769 cases of people with “normal” virus to compare them to. They chose these so that median age and proporion of females was the same. That’s why it’s called a “matched cohort study”
They then compared hospitalizations for the two groups:
Overall 42 people were hopsitalized,
16 with the variant
26 with wild-type
The difference between the two was not significant.
Read 10 tweets
28 Dec 20
"This is a moment for all of us to reflect on the toll the pandemic has taken, the progress we have made, the lessons we have learned and what we need to do in the year ahead to end this pandemic”, says @DrTedros in last @WHO #covid19 presser of the year.
@DrTedros @WHO "Science is at the core of everything we do and it has advanced at a blistering speed this year”, says @drtedros.
@DrTedros @WHO "There will be setbacks and new challenges in the year ahead”, says @DrTedros. "For example, new variants of #COVID19 and helping people who are tired of the pandemic continue to combat it."
Read 21 tweets
26 Dec 20
For all those still arguing that “only" around 0,1% of people infected with #covid19 die:
This is nonsense!
The US has around 330 million people and it has now recorded more than 330,000 deaths.
That means 0,1% of the *entire population* has died. And #sarscov2 still spreading.
about 66 million people
more than 69,000 deaths from #covid19

France: about 67 million people
more than 62,000 deaths

about 126 million population
more than 121,000 deaths

Even worse:
11,5 million population
more than 19,000 deaths
We had a lot of good data already showing that the IFR of #covid19 is much higher than 0,1%.

Now we have a lot of places where around 0,1% of the entire population have died and the virus is still spreading.

So anyone still telling this lie, is deliberately ignoring reality.
Read 5 tweets
24 Dec 20
What do we know about the new #SARSCoV2 variants? How worried should we be? What does it mean?
I promised to summarize the main points from my reporting over the last few days.
So here is my latest story and a thread (and then it’s Christmas)
First: I’ve said “We don’t know yet” a lot over the last few days and we still don’t know most of what we want to know about these variants. Getting good answers takes times. Science takes time. But we are learning a lot fast and we know a lot more today than three days ago.
The UK variant:
I explained how B.1.1.7 caught scientists’ attention in my first story on this and why they were worried (sciencemag.org/news/2020/12/m…).
That worry has only increased. There is now more data available and it points to this variant really being more transmissible.
Read 20 tweets
22 Dec 20
Some good news (and incredibly fast work) on one of the mutations scientists are worried about: N501Y.
In these lab experiments serum from recovered #covid19 patients was just as good at neutralizing virus with the mutation as without it.
This does not say anything about whether the mutation could make the virus more transmissible but it suggest the mutation alone at least does not mean the virus can widely infect people again.
Of course, both UK and SA variant have several additional mutations...
I will let other people figure out how to cite a tweet in a scientific publication ;)
Read 5 tweets

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