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?

@MarshaBradyo

Some of the tests are not picking up the new strain so harder to monitor nosocomial rates.

Can you say which tests are not picking it up?

Max lab testing isn’t picking it up.

@justanotherneighinparadise

It’s going to be interesting to see if hospital cases fail to go up inline with infections. Anecdotally we seem to be hearing more mild infections. I guess time is going to tell.

Hospitals are overwhelmed in South East and pretty close in London and East of England. Nothing milder but definitely better at early intervention and treatment with Dexamethasone and CPAP. Improvement in outcomes because of this for many. Hospital admission lag community spike by about a fortnight. Critical care spike a week after that.

Tests done at the hospital my DD works in (ICU nurse) are clearly picking up and identifying the new strain.

I don't think it's milder infections. I think it's what was said all along, that for most people it's not a serious illness (or asymptomatic), but because this version is more transmissible, higher numbers of people with it are more visible (due in part to much increased testing capacity compared to March/April). Unfortunately I think we will see an increase in both hospital admissions with serious illness and associated deaths. But we have to just wait for more data.

It’s certainly gunning for the vulnerable isn’t it 😔

[quote Turquoisesofa]www.aljazeera.com/news/2020/12/21/new-covid-strain-six-key-questions-answered[/quote]

Thank you for this. Reading it, you realise that there's the weight of the world on our shoulders in dealing with this effectively, other countries looking to the U.K. to get things under control before they'll allow travel.

Reading it, you realise that there's the weight of the world on our shoulders in dealing with this effectively, other countries looking to the U.K. to get things under control before they'll allow travel.

What can we do? We can’t eradicate the new strain?

Adequate Testing and quarantine measures.

@Chaotic45

This doesn't say that tests aren't picking up the new variant but ...I wonder if this article might be what has given rise to that idea . It discusses unusual test results which had missed one of the genes that the test usua;lly identifies .

On Friday 11 December I was alerted to the fact that a large number of the samples showing positive in our Covid-19 testing laboratory in Birmingham were unusual. Like the other Lighthouse laboratories, dedicated to testing samples from the wider public, we are on the lookout for the presence of three particular genes, with a positive Covid-19 result requiring clean detection of two of the three.

That Friday around 25% of all our positives were completely missing one of those genes – the S gene, which encodes the spike protein of the virus and is essential for viral attachment and entry into cells. It is not unusual to see some S gene drop-outs in positive samples, but usually in around 1-2% of them, not in 25%.

www.theguardian.com/commentisfree/2020/dec/22/new-coronavirus-variant-b117-transmitting

I don't understand the science and I'm v tired so apologies if I'm way off mark .

@Turquoisesofa and @peridito thank you for that information it is much appreciated.

Some good news about az vaccine from the guardian copier below

AstraZeneca says its vaccine should be effective against new coronavirus variant

British drugmaker AstraZeneca told Reuters its Covid-19 vaccine should be effective against the new coronavirus variant, adding that studies were underway to fully probe the impact of the mutation.

“AZD1222 (AstraZeneca’s vaccine candidate) contains the genetic material of the SARS-CoV-2 virus spike protein, and the changes to the genetic code seen in this new viral strain do not appear to change the structure of the spike protein,” an AstraZeneca spokesperson said.

peridito - not my source which was more reliable. Not from a newspaper at all.

Another possible utterly stupid question

I've been reading more and more this strain actually took off during lockdown.

I'm all for lockdowns if needed. But I wonder if it needed to become more transmissible to keep itself going because of lockdown? Is that a possibility?

@NeurotreeWenceslas

Adequate Testing and quarantine measures.

If it’s been around since September it’s probably in multiple countries worldwide by now.

[quote Nellodee]This article was very informative about how the new variant was discovered and why, although it has been around since September, it was only brought up as a problem in the last couple of weeks.

www.theguardian.com/commentisfree/2020/dec/22/new-coronavirus-variant-b117-transmitting[/quote]
"we are on the lookout for the presence of three particular genes, with a positive Covid-19 result requiring clean detection of two of the three"
Doesn't this imply that there'll be an increase in false negative tests on the new variant too? If there's not a 'clean detection' on one of the other 2 genes they look out for, and the S gene is missing, wouldn't those positives be missed by the tests because there's only a 'clean detection' of 1/3?

@itsgettingweird

Another possible utterly stupid question

I've been reading more and more this strain actually took off during lockdown.

I'm all for lockdowns if needed. But I wonder if it needed to become more transmissible to keep itself going because of lockdown? Is that a possibility?

Isn't the most likely place to be infected in your own home?

Isn't the most likely place to be infected in your own home?

The most likely person to give it to you is someone you spend lots of time with, without a mask, in unventilated rooms.
Which for most people equates to their household as the person they do most associating like that.

But someone has to initially bring it into the household. So if none of the household are mixing with anyone, then that's going to solve that one.

If it’s been around since September it’s probably in multiple countries worldwide by now.

I’m not so sure about that. It originated in Kent. We were in national lockdown, then straight into tier 3 and now tier 4. Travel opportunities have been limited outside of work. I myself cancelled a week’s stay in a cottage in Devon that I had slated for the beginning of December.

I mean, clearly it’s got out. It’s been sequenced in the Netherlands, Australia, and Italy. But enough to get a foothold? I hope not.

If it has got out and spread widely the decision not to put London into Tier 3 with Kent might prove the fateful one.

If it’s been around since September it’s probably in multiple countries worldwide by now

its more subtle than that. each person infected has a mixture of variants, and the fit ones get reproduced and exhaled. during reproduction a minority always mutates, and so it goes on. there have been thousands of mutations, some causing protein sequence changes. each individual virus particle has its own combination of protein changes.

spike protein double deletion Δ H69/V70 for increasing infectivity
is the mutation, but its present in quite a few isolates.(deletion of amino acids 69 and 70)

B.1.1.7, is comprised of over 1400 SARS-CoV-2 genome sequences from the UK and includes eight S gene mutations: RBD (N501Y and A570D), S1 (delH69/V70 and del144/145) and S2 (P681H, T716I, S982A and D1118H).

maybe the specific combination is important. info is from preprint
www.biorxiv.org/content/10.1101/2020.12.14.422555v3

image of amino acids of spike protein (reference sequence) from www.gisaid.org/hcov19-mutation-dashboard/

[quote SRYnegative]If it’s been around since September it’s probably in multiple countries worldwide by now

its more subtle than that. each person infected has a mixture of variants, and the fit ones get reproduced and exhaled. during reproduction a minority always mutates, and so it goes on. there have been thousands of mutations, some causing protein sequence changes. each individual virus particle has its own combination of protein changes.

spike protein double deletion Δ H69/V70 for increasing infectivity
is the mutation, but its present in quite a few isolates.(deletion of amino acids 69 and 70)

B.1.1.7, is comprised of over 1400 SARS-CoV-2 genome sequences from the UK and includes eight S gene mutations: RBD (N501Y and A570D), S1 (delH69/V70 and del144/145) and S2 (P681H, T716I, S982A and D1118H).

maybe the specific combination is important. info is from preprint
www.biorxiv.org/content/10.1101/2020.12.14.422555v3

image of amino acids of spike protein (reference sequence) from www.gisaid.org/hcov19-mutation-dashboard/[/quote]

Oh yes of course. Presumably the new strain has already mutated somewhat?

@Witchend

Isn't the most likely place to be infected in your own home?

The most likely person to give it to you is someone you spend lots of time with, without a mask, in unventilated rooms.
Which for most people equates to their household as the person they do most associating like that.

But someone has to initially bring it into the household. So if none of the household are mixing with anyone, then that's going to solve that one.

That's my line do thinking.

We had such measures that the only place with none and where transmission could take place was schools mostly.

I have no scientific knowledge but wonder if after it mutated in the immunicomoeomused person it became the dominant strain as it had to transmit faster to keep it going.

"we are on the lookout for the presence of three particular genes, with a positive Covid-19 result requiring clean detection of two of the three"

Doesn't this imply that there'll be an increase in false negative tests on the new variant too? If there's not a 'clean detection' on one of the other 2 genes they look out for, and the S gene is missing, wouldn't those positives be missed by the tests because there's only a 'clean detection' of 1/3?

Aargh Foolshapedheart that's what my extremely unscientific mind thinks as well .

Anyone help dispel the idea ?

From the Washington Post;

"Several top infectious-disease experts said the variant may not have originated in the United Kingdom. Instead, it may have been identified there first because the United Kingdom has a robust monitoring system that has examined tens of thousands of genomic sequences of virus samples.

The United States has lagged in sequencing and does not have nearly the same level of virus surveillance.

“It may very well be here. It may have even started here. The sequencing in the U.S. is so sporadic,” said Jeremy Luban, a virologist at the University of Massachusetts Medical School.

It makes sense that it was detected first in the U.K. because they have probably the world’s best surveillance program. It would not shock me at all to find out that it also is circulating in the U.S.,” said Angela Rasmussen, a virologist at the Georgetown Center for Global Health Science and Security."

New variant is already almost certainly across EU. Patient zero almost certainly in East England. Most other worrying variant in South Africa but also "explosive growth" in Nigeria - Nervtag.

Some evidence children more infectious with new variant but too soon to be sure and too soon to say whether outcomes any worse.

Not clear whether new variant leads to more asymptomatic transmission but some suggestion that it could mirror Singapore outbreak of a variant that was spread by those with milder version.
mobile.twitter.com/elliotttimes/status/1341706096612880385