New Covid Variants

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jimbob
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Re: New Covid Variants

Post by jimbob » Fri May 21, 2021 9:02 pm

badger wrote:
Thu May 20, 2021 9:58 pm
Woodchopper wrote:
Thu May 20, 2021 9:15 pm
3,424 B.1.617.2 cases in a week, an increase of 2,111 cases in a week. Not good.

https://www.gov.uk/government/publicati ... cases-data
3,424 cases to date, no? And 2,111 of them identified in the last week (12-19 May)? Or am I reading their table incorrectly?

Still not good, of course...
It's worse.
Have you considered stupidity as an explanation

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Martin Y
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Re: New Covid Variants

Post by Martin Y » Sat May 22, 2021 11:19 pm

Narendra Modi's highly effective government has swung into action and defeated the India variant at a stroke, by demanding social media firms stop calling B.1.617 the "India variant" as they have decided this will henceforth be false information.

https://www.bbc.co.uk/news/world-asia-india-57213046

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Re: New Covid Variants

Post by Herainestold » Sun May 23, 2021 12:22 am

Martin Y wrote:
Sat May 22, 2021 11:19 pm
Narendra Modi's highly effective government has swung into action and defeated the India variant at a stroke, by demanding social media firms stop calling B.1.617 the "India variant" as they have decided this will henceforth be false information.

https://www.bbc.co.uk/news/world-asia-india-57213046
Well I sort of agree, that it is stigmatizing to call it the India variant. Lets call it the Modi variant.
Double dose. Double mask. Double distance

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Re: New Covid Variants

Post by shpalman » Sun May 23, 2021 7:41 am

Herainestold wrote:
Sun May 23, 2021 12:22 am
Martin Y wrote:
Sat May 22, 2021 11:19 pm
Narendra Modi's highly effective government has swung into action and defeated the India variant at a stroke, by demanding social media firms stop calling B.1.617 the "India variant" as they have decided this will henceforth be false information.

https://www.bbc.co.uk/news/world-asia-india-57213046
Well I sort of agree, that it is stigmatizing to call it the India variant. Lets call it the Modi-fication.
FIFY
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Woodchopper
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Re: New Covid Variants

Post by Woodchopper » Sun May 23, 2021 11:56 am

New Public Health England report on the variants of concern.

https://assets.publishing.service.gov.u ... ngland.pdf

Fifty per cent of all sequenced tests are of B.1.617.2 (though this number may be influenced by travelers from India etc).

There has been rapid growth of B.1.617.2 in all regions, with the majority of cases in almost all from community transmission and not people who have travelled from India.

Secondary attack rate (the proportion of of people infected by a contact) is 12.5% for B.1.617.2 compared to 8.1% for B.1.1.7.

Relative rate of growth of B.1.617.2 is twice that of B.1.1.7.

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Re: New Covid Variants

Post by Woodchopper » Sun May 23, 2021 11:59 am

Investigation of SARS-CoV-2 variants of concern: variant risk assessments
https://www.gov.uk/government/publicati ... ssessments
National vaccine effectiveness monitoring shows a reduction in vaccine effectiveness against symptomatic infection after 1 dose of vaccine for B.1.617.2 compared to B.1.1.7 (moderate confidence). Current data suggest this is an absolute reduction of approximately 20% after 1 dose.

Vaccine effectiveness is higher and similar between variants after 2 doses with a possible small reduction for B.1.617.2 (low confidence).Although this is observational data subject to some biases, it holds true across several analytic approaches, is consistent with observed outbreaks, and is supported by pseudovirus and live virus neutralisation data. There are no data on whether prevention of transmission is affected. There are insufficient data on vaccine effectiveness against severe disease. Based on neutralisation data, vaccines are expected to remain effectiveagainst severe disease. Monitoring continues.

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Re: New Covid Variants

Post by Woodchopper » Sun May 23, 2021 12:25 pm

No 10 ‘tried to block’ data on spread of new Covid variant in English schools
Scientists, unions and teachers concerned after data cut from Public Health England report ahead of shift on face masks
https://www.theguardian.com/world/2021/ ... sh-schools


Important thread:
https://twitter.com/dgurdasani1/status/ ... 75171?s=20

Data is not looking so good on immune escape, especially for the AZ vaccine. PHE report appears to have been spun to paint a rosy picture, and publication delayed.

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Woodchopper
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Re: New Covid Variants

Post by Woodchopper » Sun May 23, 2021 1:39 pm

Abstract
Background The B.1.617.2 COVID-19 variant has contributed to the surge in cases in India and has now been detected across the globe, including a notable increase in cases in the UK. We estimate the effectiveness of the BNT162b2 and ChAdOx1 COVID-19 vaccines against this variant.

Methods
A test negative case control design was used to estimate the effectiveness of vaccination against symptomatic disease with both variants over the period that B.1.617.2 began circulating with cases identified based on sequencing and S-gene target status. Data on all symptomatic sequenced cases of COVID-19 in England was used to estimate the proportion of cases with B.1.617.2 compared to the predominant strain (B.1.1.7) by vaccination status.

Results
Effectiveness was notably lower after 1 dose of vaccine with B.1.617.2 cases 33.5% (95%CI:20.6 to 44.3) compared to B.1.1.7 cases 51.1% (95%CI: 47.3 to 54.7) with similar results for both vaccines. With BNT162b2 2 dose effectiveness reduced from 93.4% (95%CI: 90.4 to 95.5) with B.1.1.7 to 87.9% (95%CI: 78.2 to 93.2) with B.1.617.2. With ChAdOx12 dose effectiveness reduced from 66.1% (95% CI: 54.0 to 75.0) with B.1.1.7 to 59.8% (95%CI: 28.9 to 77.3) with B.1.617.2.Sequenced cases detected after 1 or 2 doses of vaccination had higher odds of infection with B.1.617.2 compared to unvaccinated cases (OR 1.40; 95%CI: 1.13-1.75).

Conclusions
After 2 doses of either vaccine there were only modest differences in vaccine effectiveness with the B.1.617.2 variant. Absolute differences in vaccine effectiveness were more marked with dose 1. This would support maximising vaccine uptake with 2doses among vulnerable groups
https://khub.net/documents/135939561/43 ... 664107ac42

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Re: New Covid Variants

Post by Woodchopper » Mon May 24, 2021 2:24 pm


raven
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Re: New Covid Variants

Post by raven » Tue May 25, 2021 10:17 am

Woodchopper wrote:
Sun May 23, 2021 12:25 pm
No 10 ‘tried to block’ data on spread of new Covid variant in English schools
Scientists, unions and teachers concerned after data cut from Public Health England report ahead of shift on face masks
https://www.theguardian.com/world/2021/ ... sh-schools
Which PHE report is that? One that looks specifically at variants, I guess.

Even if they're suppressing the local data, the PHE weekly flu & covid surveillance reports (here ) are still coming out and those definitely show there's been a speedy take off of cases in 10-19 yr olds in the NW. There's a rise in that age in the East Midlands too. The NW is the only region where cases are taking off in people of Indian/Pakistan origin, so it seems pretty likely that at least some of that is the Indian variant. I don't know how they hope to hide it.

There's 58 clusters/outbreaks associated with educational settings in wk19 (iirc that's 5 or more linked cases) - none in nurseries, 25 in Primary, 22 in Secondary, 5 in Sp schools, 6 in college/unis. For comparison, there were 53 clusters in wk18, 27 in wk17, 9 in wk16, 11 in wk15, 6 in wk14, 46 in wk13, 107 in wk12. (Spot Easter there) So 58 is not too dramatic, but there's no indication of how many cases we're talking in each cluster.

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Re: New Covid Variants

Post by Bird on a Fire » Tue May 25, 2021 10:37 am

Suppressing data is a terrible look. Seems like Johnson has been taking lessons from China.
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Re: New Covid Variants

Post by raven » Tue May 25, 2021 11:05 am

They're not supressing it. It's just late. Or something.

Just like the second National Surveillance report in October was late, and then never published because they amalgamated it with flu surveillance one and stuck it on a different webpage. Just like they kept changing the format of the main dashboard, changing the data, changing the way they recorded deaths from 60 to 28 days, etc etc.

It's all just coincidence that these things seem to happen just when whatever Johnson has decided to do is in conflict with what all the experts are saying.

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Re: New Covid Variants

Post by hakwright » Tue May 25, 2021 12:52 pm

Woodchopper wrote:
Mon May 24, 2021 2:24 pm
Another good thread
https://twitter.com/chrischirp/status/1 ... 72644?s=21
Very useful (and somewhat frightening) breakdown of the situation. The main take-aways for me are: (1) the lower efficacy of vaccines against B1617.2 after 1 dose, and (2) the fact that the proportion of people in the UK who have been fully vaccinated for at least two weeks is still fairly low. As well as the fact that the new variant is, as of now, the dominant variant in England.

I have my 2nd dose scheduled for early July. Just the wrong side of 50 to be able to bring it forward :-(

I'll definitely be much more careful until then.

Howard

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Re: New Covid Variants

Post by Herainestold » Tue May 25, 2021 4:03 pm

hakwright wrote:
Tue May 25, 2021 12:52 pm
Woodchopper wrote:
Mon May 24, 2021 2:24 pm
Another good thread
https://twitter.com/chrischirp/status/1 ... 72644?s=21
Very useful (and somewhat frightening) breakdown of the situation. The main take-aways for me are: (1) the lower efficacy of vaccines against B1617.2 after 1 dose, and (2) the fact that the proportion of people in the UK who have been fully vaccinated for at least two weeks is still fairly low. As well as the fact that the new variant is, as of now, the dominant variant in England.

I have my 2nd dose scheduled for early July. Just the wrong side of 50 to be able to bring it forward :-(

I'll definitely be much more careful until then.

Howard
We could be in lockdown again by June 21. It would better to do it now and get this variant under control.
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Woodchopper
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Re: New Covid Variants

Post by Woodchopper » Tue May 25, 2021 8:52 pm

Sanger data tells a similar story. B.1.167.2 spreading rapidly throughout England and Wales.

Now about half of all cases.

Curve seems to be flattening in London for reasons unknown.

https://twitter.com/chrischirp/status/1 ... 04768?s=21

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Re: New Covid Variants

Post by Woodchopper » Thu May 27, 2021 9:35 pm

Thread
B.1617.2 is fuelling a third wave in the UK, with not only cases but also hospital admissions rising.

Vaccines will make this wave different to those that have come before, but it remains a concern, and one that other countries will soon face.

If we plot B.1.1.7 and B.1.617.2 on a common baseline, most areas show a shrinking outbreak of B.1.1.7 alongside a growing one of B.1.617.2.

What looks like "cases are flat", is probably "one going down, other going up, and it has more room to grow than the other has to shrink".

• B.1.617.2 has sent cases rising again even in a country with very good vaccine coverage

• But vaccines are keeping cases and hospital admissions largely among the younger age groups whose risk of deaths from Covid is much lower
https://twitter.com/jburnmurdoch/status ... 10818?s=21

Much more at the link

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Re: New Covid Variants

Post by Woodchopper » Thu May 27, 2021 10:02 pm

SARS-CoV-2 variants of concern and variants under investigation in England
Technical briefing 13
27 May 2021
https://assets.publishing.service.gov.u ... ngland.pdf

SARS-CoV-2 variant data update, England
Version 3
27 May 2021
https://assets.publishing.service.gov.u ... date_3.pdf

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Re: New Covid Variants

Post by Woodchopper » Fri May 28, 2021 4:54 am


Reduced sensitivity of infectious SARS-CoV-2 variant B.1.617.2 to monoclonal antibodies and sera from convalescent and vaccinated individuals

The SARS-CoV-2 B.1.617 lineage emerged in October 2020 in India. It has since then become dominant in some indian regions and further spread to many countries. The lineage includes three main subtypes (B1.617.1, B.1617.2 and B.1.617.3), which harbour diverse Spike mutations in the N-terminal domain (NTD) and the receptor binding domain (RBD) which may increase their immune evasion potential. B.1.617.2 is believed to spread faster than the other versions. Here, we isolated infectious B.1.617.2 from a traveller returning from India. We examined its sensitivity to monoclonal antibodies (mAbs) and to antibodies present in sera from COVID-19 convalescent individuals or vaccine recipients, in comparison to other viral lineages. B.1.617.2 was resistant to neutralization by some anti-NTD and anti-RBD mAbs, including Bamlanivimab, which were impaired in binding to the B.1.617.2 Spike. Sera from convalescent patients collected up to 12 months post symptoms and from Pfizer Comirnaty vaccine recipients were 3 to 6 fold less potent against B.1.617.2, relative to B.1.1.7. Sera from individuals having received one dose of AstraZeneca Vaxzevria barely inhibited B.1.617.2. Thus, B.1.617.2 spread is associated with an escape to antibodies targeting non-RBD and RBD Spike epitopes.


[Emphasis added]
Finding re. the AZ vaccine ties in with UK data linked to earlier.

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Re: New Covid Variants

Post by jimbob » Fri May 28, 2021 10:50 am

Woodchopper wrote:
Fri May 28, 2021 4:54 am

Reduced sensitivity of infectious SARS-CoV-2 variant B.1.617.2 to monoclonal antibodies and sera from convalescent and vaccinated individuals

The SARS-CoV-2 B.1.617 lineage emerged in October 2020 in India. It has since then become dominant in some indian regions and further spread to many countries. The lineage includes three main subtypes (B1.617.1, B.1617.2 and B.1.617.3), which harbour diverse Spike mutations in the N-terminal domain (NTD) and the receptor binding domain (RBD) which may increase their immune evasion potential. B.1.617.2 is believed to spread faster than the other versions. Here, we isolated infectious B.1.617.2 from a traveller returning from India. We examined its sensitivity to monoclonal antibodies (mAbs) and to antibodies present in sera from COVID-19 convalescent individuals or vaccine recipients, in comparison to other viral lineages. B.1.617.2 was resistant to neutralization by some anti-NTD and anti-RBD mAbs, including Bamlanivimab, which were impaired in binding to the B.1.617.2 Spike. Sera from convalescent patients collected up to 12 months post symptoms and from Pfizer Comirnaty vaccine recipients were 3 to 6 fold less potent against B.1.617.2, relative to B.1.1.7. Sera from individuals having received one dose of AstraZeneca Vaxzevria barely inhibited B.1.617.2. Thus, B.1.617.2 spread is associated with an escape to antibodies targeting non-RBD and RBD Spike epitopes.


[Emphasis added]
Finding re. the AZ vaccine ties in with UK data linked to earlier.

That's really not good
Have you considered stupidity as an explanation

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Re: New Covid Variants

Post by raven » Fri May 28, 2021 12:35 pm

Woodchopper wrote:
Thu May 27, 2021 9:35 pm
Thread

https://twitter.com/jburnmurdoch/status ... 10818?s=21

Much more at the link
That's an excellent thread. Plenty of graphs. I love graphs.

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Re: New Covid Variants

Post by Herainestold » Sat May 29, 2021 3:52 am

No point in regional restrictions now, the genie is out of the bottle.
The only way to avoid a catastrophe is to go back to a national lockdown.

65% of the country un vaccinated.(two doses)

We are in big trouble.
Double dose. Double mask. Double distance

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Re: New Covid Variants

Post by Grumble » Sat May 29, 2021 1:00 pm

Herainestold wrote:
Sat May 29, 2021 3:52 am
No point in regional restrictions now, the genie is out of the bottle.
The only way to avoid a catastrophe is to go back to a national lockdown.

65% of the country un vaccinated.(two doses)

We are in big trouble.
Only 53.5% of the eligible groups (adults) on less than two doses.
https://coronavirus.data.gov.uk/
You’ve got no chutzpah, your organisational skills are lacklustre and your timekeeping is abysmal.

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Re: New Covid Variants

Post by Woodchopper » Mon May 31, 2021 2:35 pm

Update thread: https://twitter.com/chrischirp/status/1 ... 15876?s=20

B.1.167.2 now the dominant strain in most of England. Case numbers and hospital admissions rising.

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Re: New Covid Variants

Post by Trinucleus » Mon May 31, 2021 7:22 pm

Woodchopper wrote:
Mon May 31, 2021 2:35 pm
Update thread: https://twitter.com/chrischirp/status/1 ... 15876?s=20

B.1.167.2 now the dominant strain in most of England. Case numbers and hospital admissions rising.
Is it fair to give % increase in case numbers when most of them are less than 20 or so? Also, in previous waves have been in unvaccinared populations, so presumably having a fair percentage fully vaccinated will slow things, particularly the death rate?

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Re: New Covid Variants

Post by raven » Mon May 31, 2021 11:42 pm

Trinucleus wrote:
Mon May 31, 2021 7:22 pm
Is it fair to give % increase in case numbers when most of them are less than 20 or so?
Horses for courses. Sometimes you want to look at %, sometimes absolute numbers. Giving both gives a fuller picture.
If we're right at the start of an exponential increase, the % increase over a fixed time like a week gives us an idea of how quickly things might be take off.

Say my local area had 2 cases last week. 100% increase per week (doubling) gives you 4 cases this week, then 8 the next, then 16, 32, etc. But if it's 300% increase per week (quadrupling) gives you 8 cases this week, then 24 the next, then 96,384, etc. Which you can see doesn't look to different at first - 4 or 8 cases sounds like no big deal - but after 4 weeks 32 or 384 cases is very different.


Yes, the numbers are small now so not only does it not seem worrying, there's also big error bars on those % in the early weeks. But the thing is in a pandemic you can't wait two or three weeks for data to accrue and give you more accuracy. This thing has an incubation period such that even if we intervene right now, measures will take about 10-14 days to take effect so in effect the increase is already baked in for that period.
Also, in previous waves have been in unvaccinared populations, so presumably having a fair percentage fully vaccinated will slow things, particularly the death rate?
You might find this helpful: https://threadreaderapp.com/thread/1399 ... 44261.html The graph scales aren't too good, but if we have a third wave with lots more infections we could, even with vaccines, still see pressure on ICU beds.

And obviously, we'll see younger people in those ICU beds too. That's what concerns me: that we haven't protected younger, working age cohorts yet and they're going to bear the brunt of it this time. Sure, not so many of them will get sick, but I don't know if the public is really prepared for wards of patients in their 20s /30s/ 40s. I'm pretty sure the staff will find that much harder too.

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