Covid 2.0

[Pinball]

It was a bullshit politician's scare tactic at the same time as London tier 3. Not a coincidence.

No evidence that vaccine efficacy will be affected AT ALL. The dynamic alpha male Chris Whitty should have been all over that BS (haha, not. Sir yes sir).

[poo]

No evidence because early days. Public health are pretty concerned about it, I can tell you that.

[Zetetic]

Spoiler alert

I'm beginning to wonder if there's a test accuracy issue involved...

[close]

[katzenjammer]

Thread about this here from someone who sounds like they might know what they're talking about

https://twitter.com/ewanbirney/status/1338616959437598720?s=20

[jobotic]

Thread about this here from someone who sounds like they might know what they're talking about

https://twitter.com/ewanbirney/status/1338616959437598720?s=20

Thanks

[Lordofthefiles]

https://news.sky.com/story/covid-19-new-coronavirus-strain-spreading-faster-than-previous-variant-government-scientists-warn-ministers-12166858

#There may be trouble ahead...#

[JarrowMonkey]

In Saturday's Telegraph then. I can wait.

Is that like being egg bound?

[Chedney Honks]

Blod, I assume this actually was what you were being understandably a bit cagey about. I guess this variant has floated down the Thames straight into your sifter.

I can't fuck off out of the place soon enough, but I also suspect this may shaft my plans again. They did make contact to say that my application had been received for processing after weeks of radio silence, so I'll just await the next delay.

😃😃😃

[Zetetic]

Is it still a slightly open question whether the massive shift in S gene distribution is actually down to a specific variant (and its descendents) outcompeting the rest?

It does seem to have happened extraordinarily recently and quickly (last two weeks?).

[BlodwynPig]

Blod, I assume this actually was what you were being understandably a bit cagey about. I guess this variant has floated down the Thames straight into your sifter.

I can't fuck off out of the place soon enough, but I also suspect this may shaft my plans again. They did make contact to say that my application had been received for processing after weeks of radio silence, so I'll just await the next delay.

😃😃😃

partly yes. I guess its in the news now. evidence its been around a lot longer though and some evidence (as may have been reported) in persistence and demographic shifts. However, having spoken to some experts, a lot is dark knowledge still. Evidence that wastewater picks up mutations is probable but I think requires a bit of luck.

[Zetetic]

evidence its been around a lot longer though

This would be a broadly good thing, right? Because it suggests that it's not a massively adaptive change - unless we also think something in the last two weeks has introduced a major selective pressure, I guess...

[Chedney Honks]

Remember in Ghostbusters 2 that river of evil ooze powered by NYC miserable bastard attitudes? Maybe this is the same but for Kent!

Remember mook?

[George Oscar Bluth II]

If it is easier to spread it would explain the jump in infections in London and the SE that happened during lockdown

[Captain Z]

Would you say it's time to crack each other's heads open and feast on the goo inside?

[Cuellar]

If it is easier to spread it would explain the jump in infections in London and the SE that happened during lockdown

Could also be because no one seems to be giving a fuck about lockdown

[jobotic]

It's all so fucking funny! ha ha

[steveh]

Analysis suggests the mutations increase the ability for it gain entry and there's a hypothesis that the variant might have occurred through convalescent plasma treatment in a chronically-infected individual. Picked these quotes but helps to read the whole thing:

The B.1.1.7 lineage carries a larger than usual number of virus genetic changes. The accrual of 14 lineage-specific amino acid replacements prior to its detection is, to date, unprecedented in the global virus genomic data for the COVID-19 pandemic. Most branches in the global phylogenetic tree of SARS-CoV-2 show no more than a few mutations and mutations accumulate at a relatively consistent rate over time. Estimates suggest that circulating SARS-CoV-2 lineages accumulate nucleotide mutations at a rate of about 1-2 mutations per month (Duchene et al. 2020).

...

High rates of mutation accumulation over short time periods have been reported previously in studies of immunodeficient or immunosuppressed patients who are chronically infected with SARS-CoV-2 (Choi et al. 2020; Avanzato et al. 2020; Kemp et al. 2020). These infections exhibit detectable SARS-CoV-2 RNA for 2-4 months or longer (although there are also reports of long infections in some immunocompetent individuals). The patients are treated with convalescent plasma (sometimes more than once) and usually also with the drug remdesivir. Virus genome sequencing of these infections reveals unusually large numbers of SNP and deletion mutations and often high ratios of non-synonymous to synonymous SNPs. Convalescent plasma is often given when patient viral loads are high, and Kemp et al. (2020) report that intra-patient virus genetic diversity increased after plasma treatment was given.

...

Table 1 provides details of the B.1.1.7 lineage-specific non-synonymous mutations and deletions. We note that many occur in the virus spike protein. These include spike position 501, one of the key contact residues in the receptor binding domain (RBD), and experimental data suggests mutation N501Y can increase ACE2 receptor affinity (Starr et al. 2020) and P681H, one of 4 residues comprising the insertion that creates a furin cleavage site between S1 and S2 in spike. The S1/S2 furin cleavage site of SARS-CoV-2 is not found in closely related coronaviruses and has been shown to promote entry into respiratory epithelial cells and transmission in animal models (Hoffmann, Kleine-Weber, and Pöhlmann 2020; Peacock et al. 2020; Zhu et al. 2020). N501Y has been associated with increased infectivity and virulence in a mouse model (Gu et al. 2020). Both N501Y and P681H have been observed independently but not to our knowledge in combination before now.

https://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

[Zetetic]

Seeing public scepticism around this, given the relationship to the Tier 4 announcements in England, from a broader set of people than usual.

Interesting how completely we can piss away any trust in politicians and the state.

[Zetetic]

https://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

Interesting, and the extent of S mutations and deletions described makes it a bit more intuitive (to an ignorant layman like me, anyway) why we're seeing dropout of S-gene detection with otherwise PCR-positive specimens.

[Uncle TechTip]

How would people being treated with plasma spread the virus? Would they have infected healthcare workers and that's how it escaped?

[steveh]

How would people being treated with plasma spread the virus? Would they have infected healthcare workers and that's how it escaped?

Can only assume that a healthcare worker got infected and then passed it on, helped by it being more easily transmitted. It says in the paper "Although such infections are rare, and onward transmission from them presumably even rarer, they are not improbable given the ongoing large number of new infections."

[BlodwynPig]

Can only assume that a healthcare worker got infected and then passed it on, helped by it being more easily transmitted. It says in the paper "Although such infections are rare, and onward transmission from them presumably even rarer, they are not improbable given the ongoing large number of new infections."

*Pangolins leave thread shaking head in disbelief*

We're doing some work next week on unbiased extent of this if we can get the sequencing labs to open up.

[Lordofthefiles]

Did anyone notice both Valance and Whitty accidentally say "the new virus... I mean variant".
Could have been the pressure of the most intense press conference of the pandemic so far I suppose.

They were passing each other some strange looks behind the PM's back too.

[Zetetic]

Some discussion of emergence of and possible selection of various spike mutations:
https://twitter.com/trvrb/status/1340409968818671616

[steveh]

There's an independently-evolved variant in South Africa which has a number of similarities to this variant. Allowing such uncontrolled spread of the virus means it's not just the everyday small mutations that are cropping up everywhere but more radical ones become more feasible too.

Immunologist saying on Twitter that the data isn't there yet to fully support these variants not having some impact on immunity or vaccines. As it says in that Twitter thread Zetetic just posted, SARS-CoV-2 vaccines will need to keep updating for the its evolution like the flu ones.

[Zetetic]

Allowing such uncontrolled spread of the virus means it's not just the everyday small mutations that are cropping up everywhere but more radical ones become more feasible too.

Mmm. I guess the "coronaviruses are a big old mess and don't mutate very much" hadn't necessarily counted on the huge reservoirs we were building up just in time for large parts of the population to have anitbodies and for the vaccines...

[bomb_dog]

Sunday papers have pictures of Boris Johnson looking 'haunted' (or as the Star has him, in a brilliant sub-wimblewrong, as a turkey clown). This continuing painting of Johnson as the sole dictator of this shitshow is starting to feel like the start of the 'PM leaves in February, but that's ok you've got a whole-new government!' (but still the same Tory cunts behind the curtain, don't look or think) level of pin-the-blame-on-the-donkey before they shuffle him out the door.

[BlodwynPig]

Sunday papers have pictures of Boris Johnson looking 'haunted' (or as the Star has him, in a brilliant sub-wimblewrong, as a turkey clown). This continuing painting of Johnson as the sole dictator of this shitshow is starting to feel like the start of the 'PM leaves in February, but that's ok you've got a whole-new government!' (but still the same Tory cunts behind the curtain, don't look or think) level of pin-the-blame-on-the-donkey before they shuffle him out the door.

The media are equally complicit, worse as they could have provided an effective opposition or at least considered response. Even our stuff was reported badly and that is because the knowledge owners are shunted to the side when comms come into play.

[BlodwynPig]

Some discussion of emergence of and possible selection of various spike mutations:
https://twitter.com/trvrb/status/1340409968818671616

Thanks Z. We've got a good (small) team on this - but fuck people are nervous as hell.

[BlodwynPig]

There's an independently-evolved variant in South Africa which has a number of similarities to this variant. Allowing such uncontrolled spread of the virus means it's not just the everyday small mutations that are cropping up everywhere but more radical ones become more feasible too.

Immunologist saying on Twitter that the data isn't there yet to fully support these variants not having some impact on immunity or vaccines. As it says in that Twitter thread Zetetic just posted, SARS-CoV-2 vaccines will need to keep updating for the its evolution like the flu ones.

As always, thank you Steve. We need you on comms - reach out in PM if you fancy doing some good work for big gov.