New strain stuff.....

[MistressoftheDarkSide]

www.theguardian.com/world/2020/dec/18/boris-johnson-calls-crisis-meeting-to-discuss-response-to-new-covid-strain

So,it's just a variant, nothing to see here, blah blah blah..... I'm pretty sanguine about this stuff but dropping this late at night as a headline right now..... I'm getting mightily pissed off with the uncertainty and the subtle fear mongering......

Any thoughts?

I read south Africa found a new varient similar characteristics to UK new one.
Affecting more younger age people and more infectious.

How do our government know its 70% more contagious?

Also I get its mainly focused London and South East however

Some left London tonight for other areas.

Also if 18cases Scotland which seems incredible low and Wales not sure how many thought Hancock said over 1000 in total with in UK Monday just gone.
How does this new variant avoid the south west ir north east that border Scotland and Wales and that you would have to travel to.
Are all other tiers at risk?
Really surprised Xmas still on for all other tiers and no English lockdown.

Do they really test each positive result to see which variant it is? 25000 tests per day? They must only check a proportion of these, surely?

If it’s more transmissible in the way so excellently described upthread, surely that also means that existing SD measures may not be enough, because some virus must go past 2m and that may now be enough to infect? Thinking mainly of workplaces here not the odd pop to the shops.

Morning all.

I just read the latest report put out yesterday evening from the Coronavirus Genomics Consortium UK (COG).

These are the people we have to thank for us being able to detect this new variant so quickly.

It’s a pretty public-friendly report, so please read.

virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563

testingtesting321 they test samples and extrapolate the results to population level.

Thank you so much for this informative thread. I find hard data very reassuring.. especially when explained in a way that I can understand!

Re: transmissiblity.

It has always been airborne. It doesn’t magically drop to the ground after 2m. Most of the larger droplets do, but not all and there are many, much smaller particles which can travel a lot further. This has always been the case.

It doesn’t only get to a threshold concentration in the air after 15 min in a room with people. It is a continuum.

We don’t have the results from the government labs to show us exactly why they say it is 70% more “contagious”/“transmissible” .

Not sure exactly what they said in the presser but there are lots of components to it. Do they mean 70% more able to get into cells ? I suspect so. I don’t think there’s been time to do any actual infection studies in animals. There is previous work on a mouse model, but that is a variant that contains the N501Y and not all the new mutations.

Biris also said it raises the “R” by 0.4.

There is a really brilliant interview here between Kate Garaway and Dr Chris van Tulleken (operation ouch). listen to him talk about how careful he is, wears lab gloves on the bus, really careful over Christmas.

We should all be being really, really careful. Whatever you were doing before, do it a bit more.

www.rsm.ac.uk/resources/covid-the-festive-season-expert-advice-for-staying-safe/

Testing they only sequence about 10% of cases in this way.

Their paper says as of 15th December there are 1623 genomes sequenced with this variant. So it means ~ 16,230 people have this one in the UK currently.

Boris also said it raises the “R” by 0.4

It'll mean they have observed an increase in secondary attack rate.

The mechanism by which that has come about may not yet be fully understood. Lower infective dose required? That strikes me as a plausible hypothesis.

Chris VT is really careful - who wouldn't be when they have seen their clone incur heart damage as a result of covid? Xander mentioned recently that his cardiac issues persist.

That report is interesting thanks. There really is an awful lot of brainpower working behind the scenes isn’t there!

Interesting to read how they think the mutation might have arisen.

Everything the light touches

Thank you so much for taking the time to explain this all so well but also scientifically but in a way we can understand.

I had a little understanding of genetics as my ds has a change on BSCL2 gene (a protein change) but your clear explanations have helped me understand more how his genetics work as well. He's in a splicing and disease study and I didn't fully understand what it meant but your explanations have helped me understand some of the terminology more.

But back to the other bit. It's been great to have a calm explanation of how COVID is spreading and why we have these measures. None of this is easy but it's easier when explanations are clear.

@everythingthelighttouches

IcedPurple “ Has 'the science' said that this variant is anything to be alarmed about though?”

“The science” isn’t a single, static thing. It is a process.

There is provisional evidence that it might be a problem. I doubt any scientists are “alarmed” yet, but many of us can see the potential for concern. The existing evidence is:

1. structural evidence- it is known some of the many mutations in this variant cause changes in the structure of the protein at important places.

1. It is known from separate studies on different variants (but which contain some of the same mutations), that the virus can “escape” the immune response. These studies were in people who were already very ill.

3.Studies in mice showed one of the mutations (N501Y) leads to increased ability to bind end enter cells

1. A different variant with the N501Y mutation has emerged completely separately in South Africa and is also becoming extremely prevalent. This, like the emergence of the new strain here, is correlation but not yet enough evidence for causation.

I have poo-poohed anything like this in the press before. However this is a bit different.

What we are all waiting for is the data from Porton Down where they will be testing this exact variant:

1. with recent human convalescent sera (naturally generated antibodies from someone’s who recently

Had covid) and

1. with vaccine-induced antibodies.
2. Binding assays
3. Looking at its ability to enter cells versus other variants

And many more experiments I can’t think of.

A whole other bunch of scientists will right now be doing some very clever computing to look at the rate at which this variant is increasing when directly compared to other variants in the same groups of people, in the same area, over the same period of time.

I love your posts. So eloquent.

[quote everythingthelighttouches]Morning all.

I just read the latest report put out yesterday evening from the Coronavirus Genomics Consortium UK (COG).

These are the people we have to thank for us being able to detect this new variant so quickly.

It’s a pretty public-friendly report, so please read.

virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563[/quote]
Thanks for this really good to get the source

Does anyone know if it is becoming less virulent? Is that the word, I mean more benign? I thought that when viruses become more contagious, they usually became less dangerous. Wouldn’t it be unusual if it maintained the same level of virulence or was as dangerous?

Looking at the data, the hospital admissions doesn’t seem to be having the same jump as the case increases? Would this support that it is becoming more benign? I know it depends on age etc, but at a macro level you’d expect to see some form of correlation?

Everything you’ve been so reassuring and insightful. I know the working assumption is that the vaccine will still work.

I trust Chris Whitty and he is very careful with his words. And I know you are too.

But I wondered what you thought about effect on vaccine?

Even if it’s a we can’t know answer - how long do you think it might take to know

Does anyone know if it is becoming less virulent? Is that the word, I mean more benign? I thought that when viruses become more contagious, they usually became less dangerous. Wouldn’t it be unusual if it maintained the same level of virulence or was as dangerous?

It's not shown any diminution.

It seems to be staying the same.

As this virus is contagious before symptoms show, there is no evolutionary pressure to refrain from killing the host, as it does not need the host to remain alive as the transmission is already achieved before they even know they are ill.

(There is even a competing evolutionary pressure - killing the host means when your fellow viruses who already jumped off into a new one, make their next jump, they don't go to waste on an immune person)

We should all be being really, really careful. Whatever you were doing before, do it a bit more.

Thank you for this explanation; it possible it lasts a little longer on surfaces for example. Or survives certain air conditions better.

In school in sept everything was constantly washed and sprayed; that had definitely begun to reduce especially as it seemed to be the message that it's more air that's the issue. I know I wasn't being quite as on top of it as I was in sept though the main things were covered. For example I had stopped wiping down my computer when I first went in. (I don't think anyone else uses it but can't be sure as I'm part time. My main issue is that I have to share a lot of equipment with different classes).

It's possible the virus has just found a way to be more contagious over and above our hygiene mitigations. That's how an evolution would work. As one more contagious mutation would naturally spread more easily.

Scaevola, thanks. So how come we aren’t seeing the subsequent increased spike correlate to hospital admissions? From the data I can see admissions are up approx ten percent but over forty percent increase in cases leading up to it. In addition testing has increased substantially during that period to detect those cases?

marsha

We don’t know yet. There are a lot of changes to the spike and some clear changes to parts of the protein previously shown to be antibody binding sites. 69/70 position deletion means a loop which previously stick out it now tucked in.

The vaccines make a lot of antibodies to stick at a lot of different spots along the spike protein.

I think it is plausible that some vaccines may not work so well but they will still work.

Remember the vaccines have shown way higher efficacy than we could ever have dreamed of.

So even if it turns out they are slightly less effective it will still be “good enough”. That’s all we need.

I’m following Gupta lab, Cambridge on Twitter.
You will get some of the most up to date information from them.

This is a reallly dim question. But I can’t get my head around the evolution of viruses, scientists talk about them like they are intelligent thinkers! How does a virus know to evolve ? How does it know it doesn’t need to become milder because the host can infect before symptoms ? This blows my mind !

neuro
“It possible it lasts a little longer on surfaces for example. Or survives certain air conditions better.”

I really doubt it. There’s absolutely no evidence for that. Not even a “smoking gun” from the structural and cell data.

That would be changes in the proteins for the capsid or envelope of the virus and that’s a completely different part of the protein to the spike.

No. If this is more transmissible, it’s because whatever is there is better able to enter the cells in your upper airways.

@tootyfruitypickle the virus doesn’t know. There will be a lot of random mutations. Every now and then a mutation will happen which means the virus spreads faster. Clearly that variant will be successful.

If a virus kills its host quickly it will be less successful than a virus which keeps its host alive for longer because then there is less time for it to spread. A virus which transmits itself when patients are asymptomatic will be more successful than one which transmits itself only when symptoms are present. Because people won’t know they have it and will spread it faster. Viruses don’t know this - it will just happen.

So how come we aren’t seeing the subsequent increased spike correlate to hospital admissions? From the data I can see admissions are up approx ten percent but over forty percent increase in cases leading up to it. In addition testing has increased substantially during that period to detect those cases?

Possibly lag.

You can test positive very shortly after infection (with results turn around is ok at the moment) but are unlikely to become ill enough to require hospitalisation until about 6-7 days in.

What concerned me about yesterday's rolling 7 day figures (even aiming off a bit for the additional Welsh figures) is that number of tests performed was up 4% but number of positives up 38%.