Scrutable

Woodchopper wrote: Mon Dec 21, 2020 9:10 am

headshot wrote: Mon Dec 21, 2020 7:44 am
There’s zero chance a new variant first detected in Sept has not spread far and wide by now...

I agree. As far as I recall, only Denmark and the Netherlands have found it so far. But most places haven't been actively looking for it...

Well, because the UK didn't tell anyone about it until just now, but it's unlikely that in September it would have been obvious that this particular mutation would turn out to be more transinfectimissicive.

A lot of places actively look for covid in people coming from different countries anyway.

shpalman wrote: Mon Dec 21, 2020 9:19 am

Woodchopper wrote: Mon Dec 21, 2020 9:10 am

headshot wrote: Mon Dec 21, 2020 7:44 am
There’s zero chance a new variant first detected in Sept has not spread far and wide by now...

I agree. As far as I recall, only Denmark and the Netherlands have found it so far. But most places haven't been actively looking for it...

Well, because the UK didn't tell anyone about it until just now, but it's unlikely that in September it would have been obvious that this particular mutation would turn out to be more transinfectimissicive.

A lot of places actively look for covid in people coming from different countries anyway.

As far as I remember from my fevered reading this morning, standard tests aren't designed to distinguish the new variant, and it has proved difficult to detect using PCR.

I think it means certain PCR tests might be less sensitive to it, depending on which bits of the viral genome they're looking for.

Of course these tests won't tell you which variant they've detected; in the UK I think they've been randomly selecting some samples for full sequencing and I suppose that in the Italian who came back from London and tested positive, they sequenced his swab to check if it was the new variant.

sTeamTraen wrote: Sun Dec 20, 2020 9:52 pm This shows up, once again, the utter folly of the herd immunity idea. The virus has the potential to mutate on every transmission (or of course, at every reproduction within someone's body), and it's completely to be expected that some of those mutations would be adaptive. More transmission, more mutations.

Absolutely. This is a selfish reason to be sh.t-scares of the spread in the US, Brazil and elsewhere.

I don't know how bad this mutation is, but imagine one that brought about a substantial increase in mortality in the age group that we might denote by the range [Julia Hartley-Brewer < N < Allison Pearson]. They would be screaming blue f.cking murder about how nobody told them that this could happen, although they've been strutting around with their newly-minted PhDs in Amateur Epidemiology for the past year.

I've probably said this on a "the next pandemic" thread somewhere, but we are so lucky that this virus affects the age profile it does, i.e. mainly very elderly people. I mean, that's pretty bad, but imagine if school-age people had the same death rate.

shpalman wrote: Mon Dec 21, 2020 9:34 am I think it means certain PCR tests might be less sensitive to it, depending on which bits of the viral genome they're looking for.

Of course these tests won't tell you which variant they've detected; in the UK I think they've been randomly selecting some samples for full sequencing and I suppose that in the Italian who came back from London and tested positive, they sequenced his swab to check if it was the new variant.

This site says the UK's covid genomics programme currently has full viral genomes for ~10% of all positive tests. I don't know how that compares to other countries, but it is a field where the UK does have top-notch capabilities, and I don't know if many countries are full genome sequencing at that scale. So there's a very strong chance that something like this has happened, or could happen, elsewhere, in a place that isn't looking so hard for it. I'm not sure how well the US is doing on this front for example.

https://www.cogconsortium.uk/news_item/ ... mutations/

On the question of sensitivity of tests to the variant, there are two questions - one is that the routine RT-PCR testing is a test for the virus, but not for which specific variants, and the other is that certain mutants might fall on the PCR primer sites and so affect detection. The tests don't rely on a single primer pair, so should be able to see past that, but I did see a comment that this variant does cause a drop-out of one of the routine primers. (I presume this is at the two-codon deletion site, which is a more significant change in sequence than a single base change. )

Sciolus wrote: Mon Dec 21, 2020 9:46 am I've probably said this on a "the next pandemic" thread somewhere, but we are so lucky that this virus affects the age profile it does, i.e. mainly very elderly people. I mean, that's pretty bad, but imagine if school-age people had the same death rate.

The "classical liberals" would be reminding us that it only kills 1.4% of the population, which in the UK is less than a million. (Or, as Stalin would put it if you believe the quote attributed to him, "a statistic".) Peanuts compared to 66 million who didn't die. Stop moaning, snowflakes.

I just read that, of 270k sars-cov2 viral genomes sequenced so far, 120k of these were from the UK sequencing consortium. That does increase the chances that the UK was just quicker to detect a faster spreading strain.

Also, this strain has already shown up in 9 cases in Denmark, so it has already started spreading more widely.

In Europe they basically just think this new variant spread a lot in England because the English are sh.t at covid containment.

The scientific data around N501Y was still unclear, Christian Drosten, a leading German virologist, told the broadcaster Deutschlandfunk on Monday. Claims that the strain was 70% more transmissible appeared to be an estimate for now, he said, and would need to be verified by British scientists over the course of this week.

Drosten said: “The question is: is this virus being boosted by a coming new wave in the region concerned [south-east England], or is this virus responsible for creating this wave in the first place? That’s an important difference.”

Drosten said the strain had also been detected in other countries such as the Netherlands, where it did not appear to have multiplied in a significantly more rapid way. “I am open to new scientific insights, and in science there are always surprises, but I am everything but worried in this respect,” he said.

In France, Vincent Enouf of the Institut Pasteur said there was no proved link between the new mutation and the more rapid spread of the virus in Britain.

“We’re told is it spreading faster in parts of the UK,” Enouf told France 2 television. “But is that the result of a super-spreader transmitting the virus, or of the new mutation? All of this still has to be verified.”

... it does not so far appear to be spreading as fast in the Netherlands as in the UK, Ab Osterhaus, emeritus professor of virology at the Erasmus University in Rotterdam, told the Algemeen Dagblad newspaper.

“In areas where the number of infections rise particularly fast, it tends to get linked to the mutation,” Ostarhaus said. “But I don’t know at all yet whether that’s justified.” ... Marion Koopmans, the head of the Erasmus department of viroscience, said, “the Netherlands is already in lockdown. That would help prevent rapid spread here.”

Just to put everyone's mind at rest a bit, we currently have NO evidence that the BioNTech/Pfizer vaccine does NOT protect against this.
The mutations in the spike proteins do not sufficiently alter their shape to make it likely that antibodies would bind to them noticeably less-well.
So, although it may be a little more transmissible, we don't have to worry that our vaccines are useless.

Cheers Tom

Italy is tracing anyone who arrived from the UK in the past two weeks to check if they've been swabbed. So far they've found 7 positives but are still checking if any of them are the new variant (apart from that known case in Rome which by the way is asymptomatic so must have been picked up by a swab at the airport on arrival).

(I arrived just over two weeks ago, with a negative mail-in test from England and a negative test at a private clinic here exactly two weeks ago, both of which I communicated to the local health service at the time.)

https://twitter.com/mugecevik/status/13 ... 6682838021

Interesting thread on this

Woodchopper wrote: Mon Dec 21, 2020 9:24 am As far as I remember from my fevered reading this morning, standard tests aren't designed to distinguish the new variant, and it has proved difficult to detect using PCR.

shpalman wrote: Mon Dec 21, 2020 9:34 am I think it means certain PCR tests might be less sensitive to it, depending on which bits of the viral genome they're looking for.

Of course these tests won't tell you which variant they've detected; in the UK I think they've been randomly selecting some samples for full sequencing and I suppose that in the Italian who came back from London and tested positive, they sequenced his swab to check if it was the new variant.

National testing data shows increased prevalence of the variant in positive cases over time. This is detected incidentally by the commonly used 3-gene PCR test because 69-70del leads to a negative signal. But this does not effect the results of the test

Is there any truth to the rumour that this new variant was picked up in a cluster which was found to centre around a secondary school? I've heard speculation that this is the case, along with theories that our poor mitigation measures in schools have led to selection pressure for a strain that is better at being transmitted by children. However, I've not seen any evidence backing this up, though a lot of the government's actions would be in line with this.

All I can find is that it was first identified in Kent on the 20th of September. e.g. https://www.abc.net.au/news/2020-12-21/ ... s/13003008

Speculation has been that it evolved within a chronic patient, since that's apparently the sort of situation which can give you so many mutations at once.

Good thread on what's known: https://twitter.com/mugecevik/status/13 ... 38021?s=20

shpalman wrote: Mon Dec 21, 2020 7:28 pm All I can find is that it was first identified in Kent on the 20th of September. e.g. https://www.abc.net.au/news/2020-12-21/ ... s/13003008

Speculation has been that it evolved within a chronic patient, since that's apparently the sort of situation which can give you so many mutations at once.

I don't think it was identified in Sept. Someone twittered that it was identifed as a problem recently, then checking backwards uncovered a sample from Sept.

shpalman wrote: Mon Dec 21, 2020 1:25 pm

In France, Vincent Enouf of the Institut Pasteur said there was no proved link between the new mutation and the more rapid spread of the virus in Britain.

“We’re told is it spreading faster in parts of the UK,” Enouf told France 2 television. “But is that the result of a super-spreader transmitting the virus, or of the new mutation? All of this still has to be verified.”

So it could just be that the UK isn't doing enouf to prevent the spread?

AMS wrote: Mon Dec 21, 2020 10:48 am
On the question of sensitivity of tests to the variant, there are two questions - one is that the routine RT-PCR testing is a test for the virus, but not for which specific variants, and the other is that certain mutants might fall on the PCR primer sites and so affect detection. The tests don't rely on a single primer pair, so should be able to see past that, but I did see a comment that this variant does cause a drop-out of one of the routine primers. (I presume this is at the two-codon deletion site, which is a more significant change in sequence than a single base change. )

From one of those excellent links Woodchopper posted upthread (the Science article):

A fortunate coincidence helped show that B.1.1.7 (also called VUI-202012/01, for the first “variant under investigation” in December 2020), appears to be spreading faster than other variants in the United Kingdom. One of the polymerase chain reaction (PCR) tests used widely in the country, called TaqPath, normally detects pieces of three genes. But viruses with 69-70del lead to a negative signal for the gene encoding the spike gene; instead only two genes show up. That means PCR tests, which the United Kingdom conducts by the hundreds of thousands daily and which are far quicker and cheaper than sequencing the entire virus, can help keep track of B.1.1.7.

ETA: Thanks to everyone posting these links, btw. This is why I come here, so I can find out this sciencey stuff

Public Health England summery:

Investigation of novel SARS-COV-2 variant
https://www.gov.uk/government/publicati ... n-20201201

sTeamTraen wrote: Mon Dec 21, 2020 9:23 pm

shpalman wrote: Mon Dec 21, 2020 1:25 pm

In France, Vincent Enouf of the Institut Pasteur said there was no proved link between the new mutation and the more rapid spread of the virus in Britain.

“We’re told is it spreading faster in parts of the UK,” Enouf told France 2 television. “But is that the result of a super-spreader transmitting the virus, or of the new mutation? All of this still has to be verified.”

So it could just be that the UK isn't doing enouf to prevent the spread?

I think it’s unlikely. The new variant has a specific mutation to the spike protein called N501Y which improves binding to ACE2. That mutation has separately evolved in South Africa and it is associated with increased transmissibility (also rapidly becoming dominant in part of SA).
See:

summary: https://www.krisp.org.za/manuscripts/KR ... _Media.pdf

paper: https://www.krisp.org.za/manuscripts/ME ... iveira.pdf

It would be a huge coincidence if N501Y didn’t actually increase transmissibility.

The problem with the UK variant is that it appears that N501Y isn’t the only mutation which increases transmissibility.

Thread on the UK and SA mutations: https://twitter.com/firefoxx66/status/1 ... 61506?s=21

Woodchopper wrote: Tue Dec 22, 2020 7:20 am

sTeamTraen wrote: Mon Dec 21, 2020 9:23 pm So it could just be that the UK isn't doing enouf to prevent the spread?

I think it’s unlikely.

Thanks, although the entire point of my comment was the lame pun on the French person's name.

Meanwhile, the ever-reliable Tom Chivers has written one of his excellent explainers.

sTeamTraen wrote: Tue Dec 22, 2020 8:22 am

Woodchopper wrote: Tue Dec 22, 2020 7:20 am

sTeamTraen wrote: Mon Dec 21, 2020 9:23 pm So it could just be that the UK isn't doing enouf to prevent the spread?

I think it’s unlikely.

Thanks, although the entire point of my comment was the lame pun on the French person's name.

Ah, missed that.

WHO summary: https://www.who.int/csr/don/21-december ... ingdom/en/