Covid 2.0

[steveh]

I thought this was new but seems it has also been around since September. Haven't seen any comparisons in its spread. Given the Nextstrain frequency chart, perhaps now losing out to the Kent variant?

[BlodwynPig]

at this rate we'll all have our own Covid-19 variant.

Covid-19 variant is for life, not just for Christmas

[Zetetic]

Another go at estimating the increased transmissibility of KentVid and implications for the next few months:
https://cmmid.github.io/topics/covid19/uk-novel-variant.html

[Bernice]

Another go at estimating the increased transmissibility of KentVid and implications for the next few months:
https://cmmid.github.io/topics/covid19/uk-novel-variant.html

Off to fucking top meself.

[Uncle TechTip]

Another go at estimating the increased transmissibility of KentVid and implications for the next few months:
https://cmmid.github.io/topics/covid19/uk-novel-variant.html

56pc more transmissible, and to get R below 1 we have to shut all education settings. Also increase vaccine rollout speed and remain like that until it's issued widely enough.

[non capisco]

Knew I should have got a haircut last week.

[Rich Uncle Skeleton]

Next strain's gone.[nb]realised misquoting Oh Mr Porter might not be very welcome in a covid thread[/nb]

[steveh]

Useful summary update on the Kent and SA variants: https://www.sciencemag.org/news/2020/12/uk-variant-puts-spotlight-immunocompromised-patients-role-covid-19-pandemic.

Covers the potential role that people with weakened immune systems may play in more radical mutations. Did wonder about a potential connection to Kent seaside towns with high Covid rates and issues of poverty, heroin use and HIV.

There's also the concern that the increase in transmissibility, particularly with the SA variant, may be enough to make spread viable where it wasn't previously, such as sub-Saharan Africa, and among the youngest age groups - see this thread on the research Zetetic linked to and the uptick being seen in the UK with young kids.

On a more positive note, consensus seems to be building that the current vaccines are still effective with these variants and data to support this will be available early in 2021.

[George Oscar Bluth II]

There's literally no argument against a really hard lockdown while we vaccinate at this point is there.

[C_Larence]

There's literally no argument against a really hard lockdown while we vaccinate at this point is there.

None that doesn't include the phrase "but the economy"

[buttgammon]

There's a conspiracy theory here - and presumably in the UK too - that the death rate has been exaggerated by people unknown and the suicide rate has been suppressed (a claim almost always made by people who took zero interest in suicide or mental health before); some people even seem to be under the impression that every single death that has taken place in the state has been included in the covid figures, which is just downright stupid. With stuff like this around, I'm sure some people would find arguments, albeit ones founded on nonsense rather than facts. As spurious as they are, these mental theories weave quite nicely into the "what about the economy?" arguments a lot of the time.

Apologies for this not entirely relevant and quite ranty post; I'm up to here with the shit I've heard recently.

[finnquark]

Yes, I was just informed of this by a barber. He told me nobody had died of it, and when I pointed out that a colleague of mine (plus several people I know) had done, he just said 'well you would say that'. Masks don't work, this is all just a test of how quickly we give our liberties away, the vaccine is microchipped and humans are really fish or (at best) lizards.

[Fambo Number Mive]

Yes, I was just informed of this by a barber. He told me nobody had died of it, and when I pointed out that a colleague of mine (plus several people I know) had done, he just said 'well you would say that'. Masks don't work, this is all just a test of how quickly we give our liberties away, the vaccine is microchipped and humans are really fish or (at best) lizards.

The barber though you were part of the "conspiracy"? Good thing he didn't take you into the back room and interrogate you.

[finnquark]

He did think that. He asked me my job, I said teacher, and he starting talking about how teachers and academics alike reject the truth, because they have vested interests and money tied up in the lies.

[imitationleather]

What does he think of Jews?

[Fambo Number Mive]

He did think that. He asked me my job, I said teacher, and he starting talking about how teachers and academics alike reject the truth, because they have vested interests and money tied up in the lies.

I guess at least he wasn't wanking.

I assume you will be attending a different barber from now on. As you left, did you wink at him and say "Now you've found out about the conspiracy, we'll have to have you killed?" Then get out your phone and pretend to ring Chris Whitty.

[His Name Is Death]

There's a conspiracy theory here - and presumably in the UK too - that the death rate has been exaggerated by people unknown and the suicide rate has been suppressed (a claim almost always made by people who took zero interest in suicide or mental health before); some people even seem to be under the impression that every single death that has taken place in the state has been included in the covid figures, which is just downright stupid. With stuff like this around, I'm sure some people would find arguments, albeit ones founded on nonsense rather than facts. As spurious as they are, these mental theories weave quite nicely into the "what about the economy?" arguments a lot of the time.

Apologies for this not entirely relevant and quite ranty post; I'm up to here with the shit I've heard recently.

I do wonder if there is an element of it going on in places where health professionals are trying to save face over how badly they treat their patients. My grandmother passed away last month, in a care home, and the cause of death was marked down as 'COVID' when it quite clearly was related to complications of dementia.[nb]My mum, who was the only one allowed to visit her, is a nurse, so she would know.[/nb] The management claimed she tested positive for COVID, for what it's worth, but there wasn't any evidence beyond that to indicate she was exhibiting symptoms (I know you can be asymptomatic, but still...).

[Zetetic]

Did dementia appear elsewhere on the death certificate?

[His Name Is Death]

Did dementia appear elsewhere on the death certificate?

Sorry, I should have said the primary cause of death was marked down as 'COVID-19'. 'Frailty, old age and dementia' did appear on the certificate as secondary. The latter was far more likely to have been the main cause, and we weren't presented with any causal evidence or explanation of how COVID had led to her passing away, just that she had tested positive shortly beforehand (however reliable that may be). The virus could certainly have been present, but only asymptomatically.

[Head Gardener]

a variant known as Covid -19°F

[Chedney Honks]

Turns out France has got the new hypervid after a French tourist brought it back from La Terre de la Crotte de Chien. Maybe more than 45% of the cunts will get vaccinated now.

LA FÊTE DE TOMBE QUAND

[Zetetic]

What Imperial reckons regarding KentViD:
https://www.imperial.ac.uk/media/imperial-college/medicine/mrc-gida/2020-12-31-COVID19-Report-42-Preprint-VOC.pdf

"There is a consensus among all analyses that [KentViD] has a substantial transmission advantage, with the estimated difference in reproduction numbers between [KentViD] and [COVID-19 Vanilla] ranging between 0.4 and 0.7, and the ratio of reproduction numbers varying between 1.4 and 1.8."

[Zetetic]

"Whilst other variants with Δ69-70 are also circulating in the UK, the absence of detection of the S gene target in an otherwise positive PCR test increasingly appears to be a highly specific marker for [KentViD]."

i.e. It is reasonable to use S-gene-dropout as a metric of its spread.

[shiftwork2]

I know it depends on the assay but are they suggesting the other two components are equally sensitive and specific for SARS-CoV-2 and the S can now be used solely to spot the new variant?  Handy if so.  Otherwise it sounds like PCR is now less useful.

Again, peer review seems to be being sacked off and replaced by reputation of researcher and institution.  Although I accept these are not normal times.

[Zetetic]

I know it depends on the assay but are they suggesting the other two components are equally sensitive and specific for SARS-CoV-2

I don't think they tackle that question at all, but I've never seen or heard anything that suggests any concern about this - including in discussions with virologists about making sense of the PCR target data we've got routine access to - for what that's worth.

It looks as though just using two targets isn't uncommon? And that targetting Spike is actually quite unusual[nb]Possibly precisely because it might not be conserved as reliably as ORF1ab, N, or E are believed to be. Those are the three genes that the WHO advise targetting, apparently.[/nb]?

[shiftwork2]

Interesting, may plough through that pre-print in the cold light of NYD if I have a moment.

[Menu]

This is the Twitter link that led me to the report. Is Tim Bale right to be as worried as he seems to be?

https://twitter.com/ProfTimBale/status/1344912493907496962

[Fambo Number Mive]

Given that many areas that have seen a steep rise in cases recently are in outer London or the London commuter belt, might the drive to get people back to the offices to ensure they buy expensive sandwiches have greatly accelerated the spread of this new variant?

[BlodwynPig]

I don't think they tackle that question at all, but I've never seen or heard anything that suggests any concern about this - including in discussions with virologists about making sense of the PCR target data we've got routine access to - for what that's worth.

It looks as though just using two targets isn't uncommon? And that targetting Spike is actually quite unusual[nb]Possibly precisely because it might not be conserved as reliably as ORF1ab, N, or E are believed to be. Those are the three genes that the WHO advise targetting, apparently.[/nb]?

Yup, we just use N1, Scotland uses N1 and E and both pretty specific. N being somewhat the best. Although the Danes saying some variability - they use RdRP which I think is not so specific.

[jobotic]

It's not going down here. Schools are shut for now and the streets are quieter but it just keeps going.

And once the rest of the country catches up with us....