New Covid Variants

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raven
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Re: New Covid Variants

Post by raven » Tue Jun 01, 2021 12:00 am

On a more positive note, Bedford might have turned the corner, and the hotspots in London don't seem to be flaring up or spreading to neighbouring areas. So perhaps surge testing and extra measures might work to contain 1.617.2.

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shpalman
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Re: New Covid Variants

Post by shpalman » Tue Jun 01, 2021 9:14 am

this is going to annoy the internet-based media

You know, the ones who still write "per cent" because they can't even find the % key, or can't be bothered with the ° in °C, let alone figure out how to write ΑΒΓΔ (or should it be αβγδ?). This will apparently reduce the σ attached to UK, South Africa, Brazil and India whose governments have all of course handled covid in an exemplary way.

(Note that the Guardian was already referring to B.1.617.2 as "the coronavirus variant first detected in India" and not just "India variant". Now they'll have to write something like "the Delta variant, which was first detected in India, also known as B.1.617.2".)
molto tricky

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bob sterman
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Re: New Covid Variants

Post by bob sterman » Tue Jun 01, 2021 9:29 am

shpalman wrote:
Tue Jun 01, 2021 9:14 am
this is going to annoy the internet-based media

You know, the ones who still write "per cent" because they can't even find the % key, or can't be bothered with the ° in °C, let alone figure out how to write ΑΒΓΔ (or should it be αβγδ?). This will apparently reduce the σ attached to UK, South Africa, Brazil and India whose governments have all of course handled covid in an exemplary way.
Surely Wuhan should have got α - and Kent β ?

Given that we're already up to ζ for variants of interest - it won't be long before we have a "New Nu variant" (or Noo noo variant?) leading to the inevitable "Who's on First?" style discussions - particularly if bovine susceptibility to the previously identified variant is confirmed.

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Re: New Covid Variants

Post by Chris Preston » Tue Jun 01, 2021 9:54 am

The variant first discovered in India has got loose in the community in Melbourne. The current evidence appears to be that it spreads a lot faster than any of the other variants we have seen. A person from the original outbreak managed to spread it to 22 people at their smallish workplace and to someone who lived around the corner from the office.

The early talk was about this variant being 5 times as infectious, but the CMO is now saying it might be worse than that. If it is not brought under control soon, it will see a suspension of the repatriation flights from India again.
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Re: New Covid Variants

Post by Gfamily » Tue Jun 01, 2021 10:14 am

People need to recognise that exponential growth starts earlier than they think
All exponential.PNG
All exponential.PNG (53.1 KiB) Viewed 458 times
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Re: New Covid Variants

Post by lpm » Tue Jun 01, 2021 11:11 am

No. Take it away. That's a horribly misleading chart that appeals to mathematicans but is self-defeating once taken into the real world.

Nobody cares about the "low growth" box and they are right not to care. Calling it exponential destroys communication. Even "increasing growth" should be called just that, it's a worry and the worry should be communicated, but calling it exponential obscures the picture.

Just use language the way that tens of millions of other people use language, don't attempt to force the language of tens of thousands onto the real world.
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Re: New Covid Variants

Post by hakwright » Tue Jun 01, 2021 12:00 pm

It's only recently been reported, but there is a new hybrid variant that has been detected in Vietnam that sounds potentially nasty. It's a hybrid of the Alpha ("UK/Kent") and Delta ("Indian") variants. The numbers of cases in Vietnam are going up extremely rapidly, time will tell whether or not this is yet another virus mutation that will spread and cause significant additional problems.

... and I couldn't agree more about the graph and use of the term "exponential growth". Maybe I'm just more sensitive to it now, but it's quite often that I hear it used on TV or on the radio (unconnected with covid), where the speaker seems to think it means "big numbers growing quickly".

When the Suez canal was blocked, there was some article online that said the numbers of ships accumulating at the entrance of the blocked canal was "growing exponentially". That would have been *very* strange if true!

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Re: New Covid Variants

Post by Gfamily » Tue Jun 01, 2021 12:01 pm

lpm wrote:
Tue Jun 01, 2021 11:11 am
No. Take it away. That's a horribly misleading chart that appeals to mathematicans but is self-defeating once taken into the real world.

Nobody cares about the "low growth" box and they are right not to care. Calling it exponential destroys communication. Even "increasing growth" should be called just that, it's a worry and the worry should be communicated, but calling it exponential obscures the picture.

Just use language the way that tens of millions of other people use language, don't attempt to force the language of tens of thousands onto the real world.
OK, we can pretend we don't have a problem.
My avatar was a scientific result that was later found to be 'mistaken' - I rarely claim to be 100% correct
ETA 5/8/20: I've been advised that the result was correct, it was the initial interpretation that needed to be withdrawn
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Re: New Covid Variants

Post by Brightonian » Tue Jun 01, 2021 1:51 pm

shpalman wrote:
Tue Jun 01, 2021 9:14 am
this is going to annoy the internet-based media

You know, the ones who still write "per cent" because they can't even find the % key, or can't be bothered with the ° in °C, let alone figure out how to write ΑΒΓΔ (or should it be αβγδ?). This will apparently reduce the σ attached to UK, South Africa, Brazil and India whose governments have all of course handled covid in an exemplary way.

(Note that the Guardian was already referring to B.1.617.2 as "the coronavirus variant first detected in India" and not just "India variant". Now they'll have to write something like "the Delta variant, which was first detected in India, also known as B.1.617.2 (or VOC-21APR-02 in the UK (except in Scotland where it's April 02))".)
Fify.

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shpalman
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Re: New Covid Variants

Post by shpalman » Tue Jun 01, 2021 1:57 pm

I suppose they'll just need to publish its entire sequence each time, to avoid ambiguity.
molto tricky

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Re: New Covid Variants

Post by basementer » Tue Jun 01, 2021 4:50 pm

hakwright wrote:
Tue Jun 01, 2021 12:00 pm
It's only recently been reported, but there is a new hybrid variant that has been detected in Vietnam that sounds potentially nasty. It's a hybrid of the Alpha ("UK/Kent") and Delta ("Indian") variants. The numbers of cases in Vietnam are going up extremely rapidly, time will tell whether or not this is yet another virus mutation that will spread and cause significant additional problems.

... and I couldn't agree more about the graph and use of the term "exponential growth". Maybe I'm just more sensitive to it now, but it's quite often that I hear it used on TV or on the radio (unconnected with covid), where the speaker seems to think it means "big numbers growing quickly".

When the Suez canal was blocked, there was some article online that said the numbers of ships accumulating at the entrance of the blocked canal was "growing exponentially". That would have been *very* strange if true!
Surely viruses can't produce hybrids? They reproduce asexually.
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Re: New Covid Variants

Post by OffTheRock » Tue Jun 01, 2021 5:09 pm

You have to admire their optimism in thinking that naming them after letters of the Greek alphabet is going to solve the problem of people referring to them by location. That horse bolted from the stable some time ago.

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Re: New Covid Variants

Post by hakwright » Wed Jun 02, 2021 12:13 pm

basementer wrote:
Tue Jun 01, 2021 4:50 pm
hakwright wrote:
Tue Jun 01, 2021 12:00 pm
It's only recently been reported, but there is a new hybrid variant that has been detected in Vietnam that sounds potentially nasty. It's a hybrid of the Alpha ("UK/Kent") and Delta ("Indian") variants. The numbers of cases in Vietnam are going up extremely rapidly, time will tell whether or not this is yet another virus mutation that will spread and cause significant additional problems.

... and I couldn't agree more about the graph and use of the term "exponential growth". Maybe I'm just more sensitive to it now, but it's quite often that I hear it used on TV or on the radio (unconnected with covid), where the speaker seems to think it means "big numbers growing quickly".

When the Suez canal was blocked, there was some article online that said the numbers of ships accumulating at the entrance of the blocked canal was "growing exponentially". That would have been *very* strange if true!
Surely viruses can't produce hybrids? They reproduce asexually.
It's been described as a "hybrid variant" in most reports I've seen. Perhaps it started off as a descendant of either the Alpha or Delta variant, and independently evolved to pick up mutations closely linked to the other? So the term hybrid describes the fact that it now has characteristics linked to two variants, rather than the mechanism it acquired them.

I agree hybrid has other meanings and could be misleading for some people...

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shpalman
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Re: New Covid Variants

Post by shpalman » Wed Jun 02, 2021 4:54 pm

What could be misleading is that there were already Alpha-, Beta-, Gamma-. and Deltacoronaviruses.

SARS-CoV-2 is a Betacoronavirus which now has Alpha, Beta, Gamma, and Delta (and other?) variants.

Britain is in talks with AstraZeneca (AZN.L) for additional doses of its COVID-19 vaccine that will have been modified to better target the Beta Betacoronavirus...
molto tricky

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Re: New Covid Variants

Post by shpalman » Wed Jun 02, 2021 4:55 pm

hakwright wrote:
Wed Jun 02, 2021 12:13 pm
basementer wrote:
Tue Jun 01, 2021 4:50 pm
hakwright wrote:
Tue Jun 01, 2021 12:00 pm
It's only recently been reported, but there is a new hybrid variant that has been detected in Vietnam that sounds potentially nasty. It's a hybrid of the Alpha ("UK/Kent") and Delta ("Indian") variants. The numbers of cases in Vietnam are going up extremely rapidly, time will tell whether or not this is yet another virus mutation that will spread and cause significant additional problems.

... and I couldn't agree more about the graph and use of the term "exponential growth". Maybe I'm just more sensitive to it now, but it's quite often that I hear it used on TV or on the radio (unconnected with covid), where the speaker seems to think it means "big numbers growing quickly".

When the Suez canal was blocked, there was some article online that said the numbers of ships accumulating at the entrance of the blocked canal was "growing exponentially". That would have been *very* strange if true!
Surely viruses can't produce hybrids? They reproduce asexually.
It's been described as a "hybrid variant" in most reports I've seen. Perhaps it started off as a descendant of either the Alpha or Delta variant, and independently evolved to pick up mutations closely linked to the other? So the term hybrid describes the fact that it now has characteristics linked to two variants, rather than the mechanism it acquired them.

I agree hybrid has other meanings and could be misleading for some people...
Can a person catch two of the covids at the same time such that the viral RNA recombines?

(I have in mind that one of the way in which bird 'flu can become human transmissible is if someone gets bird 'flu and human 'flu at the same time, or something.)
molto tricky

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bob sterman
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Re: New Covid Variants

Post by bob sterman » Wed Jun 02, 2021 5:22 pm

shpalman wrote:
Wed Jun 02, 2021 4:54 pm
What could be misleading is that there were already Alpha-, Beta-, Gamma-. and Deltacoronaviruses.

SARS-CoV-2 is a Betacoronavirus which now has Alpha, Beta, Gamma, and Delta (and other?) variants.
It's worse than that! There are 4 betacoronavirus lineages A, B, C, D - and SARS‑CoV‑2 is in the B lineage.

So the variant formerly known as South African - is the beta variant, of a virus in lineage B of the betacoronaviruses.

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bob sterman
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Re: New Covid Variants

Post by bob sterman » Wed Jun 02, 2021 5:27 pm

shpalman wrote:
Wed Jun 02, 2021 4:55 pm
Can a person catch two of the covids at the same time such that the viral RNA recombines?
Can evolve multiple strains within a single person....

SARS-CoV-2 evolution during treatment of chronic infection
https://www.nature.com/articles/s41586-021-03291-y
...after convalescent plasma therapy, we observed large, dynamic shifts in the viral population, with the emergence of a dominant viral strain that contained a substitution (D796H) in the S2 subunit and a deletion (ΔH69/ΔV70) in the S1 N-terminal domain of the spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype were reduced in frequency, before returning during a final, unsuccessful course of convalescent plasma treatment.
But...
...we detected no evidence of recombination, based on two independent methods

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Re: New Covid Variants

Post by Woodchopper » Wed Jun 02, 2021 8:47 pm

Thread

I estimate that the new variant has a transmissibility advantage of about 70% and the respective R numbers are around 0.9 and 1.5, though with some regional differences. That corresponds to a doubling time of B.1.617.2 of about 8 days.

[...]

Unless something changes there are going to be a lot of cases.
https://twitter.com/alexselby1770/statu ... 69768?s=21

See earlier posts for the circa one week doubling time.

To recap, the recent SAGE modelling had the most pessimistic scenario at 50% more contagious.

https://twitter.com/dgurdasani1/status/ ... 16928?s=21

70% is bad bad bad.

ETA similar estimate from someone else using the Sanger data: https://twitter.com/twenseleers/status/ ... 80384?s=21

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Re: New Covid Variants

Post by Herainestold » Wed Jun 02, 2021 8:49 pm

Woodchopper wrote:
Wed Jun 02, 2021 8:47 pm
Thread

I estimate that the new variant has a transmissibility advantage of about 70% and the respective R numbers are around 0.9 and 1.5, though with some regional differences. That corresponds to a doubling time of B.1.617.2 of about 8 days.

[...]

Unless something changes there are going to be a lot of cases.
https://twitter.com/alexselby1770/statu ... 69768?s=21

See earlier posts for the circa one week doubling time.

To recap, the recent SAGE modelling had the most pessimistic scenario at 50% more contagious.

https://twitter.com/dgurdasani1/status/ ... 16928?s=21

70% is bad bad bad.
We are in big trouble.
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Re: New Covid Variants

Post by jimbob » Wed Jun 02, 2021 9:12 pm

Bolton by age groups

Image

And England by age groups

Image
Have you considered stupidity as an explanation

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Re: New Covid Variants

Post by jdc » Wed Jun 02, 2021 9:42 pm

hakwright wrote:
Wed Jun 02, 2021 12:13 pm
basementer wrote:
Tue Jun 01, 2021 4:50 pm
hakwright wrote:
Tue Jun 01, 2021 12:00 pm
It's only recently been reported, but there is a new hybrid variant that has been detected in Vietnam that sounds potentially nasty. It's a hybrid of the Alpha ("UK/Kent") and Delta ("Indian") variants. The numbers of cases in Vietnam are going up extremely rapidly, time will tell whether or not this is yet another virus mutation that will spread and cause significant additional problems.

... and I couldn't agree more about the graph and use of the term "exponential growth". Maybe I'm just more sensitive to it now, but it's quite often that I hear it used on TV or on the radio (unconnected with covid), where the speaker seems to think it means "big numbers growing quickly".

When the Suez canal was blocked, there was some article online that said the numbers of ships accumulating at the entrance of the blocked canal was "growing exponentially". That would have been *very* strange if true!
Surely viruses can't produce hybrids? They reproduce asexually.
It's been described as a "hybrid variant" in most reports I've seen. Perhaps it started off as a descendant of either the Alpha or Delta variant, and independently evolved to pick up mutations closely linked to the other? So the term hybrid describes the fact that it now has characteristics linked to two variants, rather than the mechanism it acquired them.

I agree hybrid has other meanings and could be misleading for some people...
WHO reckon it's Delta with an extra mutation:
From the WHO’s current understanding, the variant detected in Vietnam was the B.1.617.2 variant, more commonly known as the India variant, possibly with an additional mutation

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shpalman
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Re: New Covid Variants

Post by shpalman » Thu Jun 03, 2021 6:38 pm

Delta variant obviously increases hospitalisations

Also, journalists are still struggling with consistent ways to refer to variants.
molto tricky


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Re: New Covid Variants

Post by Woodchopper » Thu Jun 03, 2021 8:02 pm

From the Technical Briefing:
Severity

Complementary analyses undertaken in England and Scotland found an increased risk of hospitalisation in cases who were S gene target positive (Scotland) or had sequence-confirmed Delta variant infection (England). Confirmatory analyses are required to confirm the magnitude of the change in risk and to explore the link to vaccination in more detail.

England

Based on a record linkage of sequence-confirmed Delta and Alpha cases in England tested between 29 March 2021 and 20 May 2021, an analysis of 38,805 sequenced cases was performed to assess the risk of hospitalisation and emergency care attendance. Using stratified Cox proportional hazard regression, there was a significantly increased risk of hospitalisation within 14 days of specimen date (HR 2.61, 95% CI 1.56-4.36, p<0.001), and emergency care attendance or hospitalisation within 14 days (HR 1.67, 1.25-2.23, p<0.001), for Delta cases compared to Alphacases after adjustment for confounders (age, sex, ethnicity, area of residence, index of multiple deprivation, week of diagnosis and vaccination status).

Scotland

In the Public Health Scotland/EAVE II study, Coxproportional hazard regression was used to estimate risk factors for the time from test to hospitalisation among individuals who tested positive.Hospitalisation with COVID-19 was defined as any admission within 14 days of a positive test or where there was a positive test within 2 days of admission.The model was adjusted for age and days from 1 April2021 as spline terms together with number of co morbid conditions, gender and vaccination status.Vaccination status was determined at the data of the PCR test. Only individual who tested positive from1April 2021 onwards (until 30 May 2021) were included in this analysis.There was an increased hazard ratio of hospitalisation for those who were S-gene positive compared with those with Sgene target failure(2.39, 95% 1.72 to 3.31).

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Re: New Covid Variants

Post by Woodchopper » Thu Jun 03, 2021 8:18 pm

Also from the Technical Briefing, from S gene dropout analysis we are looking at the Delta variant being over 90% of cases in all regions except the South West and Yorkshire and Humber.

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