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[Louis MacNeice]

Would that be this Andy Wigmore?

View attachment 246095

 

[2hats]

2hats and others, thought you might be interested: I admitted someone last night who was 7 days post vaccination who was community pcr positive. I don't think he had coronavirus and think it was false positive. I contacted the PHE virologist who said it is possible : the pcr target in the community testing is just for the spike protein so it is implausible but possible that this was being picked up (but why would it be detected in mucosal surfaces?), but our in-hospital pcr testing has multiple targets and if only the spike is positive then it gets reported as negative.
Interesting if our confirmatory test is negative - we'll be writing that one up and letting PHE know ASAP!
(well, I'll be a bit delayed as my girlfriend tested positive at 5am so I'm now isolating...)

Very interesting. Post first dose of BNT162b2, presumably? Of course, absence of S is a proxy for B.1.1.7...

 

[elbows]

Very interesting. Post first dose of BNT162b2, presumably? Of course, absence of S is a proxy for B.1.1.7...

I'm confused about the bit about community PCR testing being just for the spike protein. Unless I've misunderstood what 'community pcr testing' is referring to I cant quite get my head round this claim that community testing only looks for spike stuff, because if that were the case then surely S-dropouts would result in a straightforward negative result - there wouldnt be other components which still test positive and thus when combined with no S positive, are assumed to be 'positive but with the new variant'.

I was under the impression that some of the large PCR processing labs use a method which tests for multiple things including S, so can deliver data that can be used as a proxy for number of new variant cases. But the labs that dont use this sort of test are still testing for other aspects, not S, rather than only for S. And S testing positive on its own isnt up to the standard that would result in a proper positive case being recorded?

 

[kropotkin]

Very interesting. Post first dose of BNT162b2, presumably? Of course, absence of S is a proxy for B.1.1.7...

Yes, after the BioNTech first dose.
I assume whether the pcr assay would pick up B.1.1.7 depends on the specific rna sequence it looks for and whether that spans the deletion. So some 'spike targets' would pick it up and some wouldn't...?

 

[elbows]

From https://assets.publishing.service.g...947048/Technical_Briefing_VOC_SH_NJL2_SH2.pdf

The UK has a high throughput national testing system for community cases based in a small number of large laboratories. Three of these laboratories use a three target assay (N, ORF1ab, S) from Thermo Fisher (TaqPath). Currently more than 97% of pillar 2 PCR tests which test negative on the S-gene target and positive on other targets are due to the VOC (cf. Section Impact on diagnostic assay below).

And I still dont understand where the idea that community PCR testing only targets S comes from, it doesnt ring true unless we are talking about some other sort of test that I havent considered.

 

[elbows]

And to be clear, I say that in part because if community PCR testing only targeted the spike then it would fail to detect the new variant and that would be a massive oh shit moment with huge ramifications for disease surveillance.

 

[2hats]

Yes, after the BioNTech first dose.
I assume whether the pcr assay would pick up B.1.1.7 depends on the specific rna sequence it looks for and whether that spans the deletion. So some 'spike targets' would pick it up and some wouldn't...?

That could indeed be the case. There are numerous assays out there, variously with 1, 2 or 3 targets. Tests from different vendors can target different sub-units on the spike as well as a range of parts of the RNA, envelope and nucleocapsid. So all a bit hand-waving without knowing the specifics of what was used here.

 

[2hats]

And I still dont understand where the idea that community PCR testing only targets S comes from, it doesnt ring true unless we are talking about some other sort of test that I havent considered.

Presumably by 'community' we are talking about some separate 'private' testing of some flavour here (which could be using a single channel assay) as oppose to the standard national testing (eg Lighthouse Labs, etc)?

 

[elbows]

That could indeed be the case. There are numerous assays out there, variously with 1, 2 or 3 targets. Tests from different vendors can target different sub-units on the spike as well as a range of parts of the RNA, envelope and nucleocapsid. So all a bit hand-waving without knowing the specifics of what was used here.

Combining that with the angle I've been going on about, and I would say its rather urgent to determine whether assays with only 1 target have been widely used as part of the UK system, and if so whether the authorities have deliberately not mentioned this when discussing the new variant?

 

[elbows]

Presumably by 'community' we are talking about some separate 'private' testing of some flavour here (which could be using a single channel assay) as oppose to the standard national testing (eg Lighthouse Labs, etc)?

I dont know, in my mind the term community testing is used to refer to Pillar 2 testing, ie non-NHS testing. A huge part of the current official national system.

 

[kropotkin]

Presumably by 'community' we are talking about some separate 'private' testing of some flavour here (which could be using a single channel assay) as oppose to the standard national testing (eg Lighthouse Labs, etc)?

It's the labs run by PHE accessed via test and trace and the app that seem to be using single-channel, according to my virology colleague

 

[elbows]

It's the labs run by PHE accessed via test and trace and the app that seem to be using single-channel, according to my virology colleague

It just doesnt sound right to me, and the most likely explanation is that something has gone wrong with what they've said or how its been interpreted.

 

[elbows]

I mean if it were true then they couldnt use the s-dropout as a proxy indicator for the new variant, they would just be getting a tonne of false negatives rather than what they actually get from new variant samples, which is positives but with the s bit coming back negative. And they've relied very heavily on that for recent analysis of new strain transmissibility and prevalence, including on a regional basis.

 

[Mation]

2hats and others, thought you might be interested: I admitted someone last night who was 7 days post vaccination who was community pcr positive. I don't think he had coronavirus and think it was false positive. I contacted the PHE virologist who said it is possible : the pcr target in the community testing is just for the spike protein so it is implausible but possible that this was being picked up (but why would it be detected in mucosal surfaces?), but our in-hospital pcr testing has multiple targets and if only the spike is positive then it gets reported as negative.
Interesting if our confirmatory test is negative - we'll be writing that one up and letting PHE know ASAP!
(well, I'll be a bit delayed as my girlfriend tested positive at 5am so I'm now isolating...)

Why do you think it was a false positive?

 

[kropotkin]

Why do you think it was a false positive?

Clinically didn't fit, enough that I'm suspicious it was false (for one reason or another- hence the interest!).
He had a normal CXR (often abnormal) and his lymphocytes were normal (usually low). Infective source was most likely an indwelling catheter.

We've had a few false +ve over the pandemic, but equally had a few with high viral load but completely asymptomatic- which he may turn out to be. It's all interesting...

 

[2hats]

It's the labs run by PHE accessed via test and trace and the app that seem to be using single-channel, according to my virology colleague

Really depends on the specifics of the test(s) concerned.

I mean if it were true then they couldnt use the s-dropout as a proxy indicator for the new variant, they would just be getting a tonne of false negatives rather than what they actually get from new variant samples, which is positives but with the s bit coming back negative. And they've relied very heavily on that for recent analysis of new strain transmissibility and prevalence, including on a regional basis.

AFAICS, all the (UK) literature on B.1.1.7 references data from Lighthouse (and affiliated labs) using the 3 channel Thermo Fisher TaqPath RT-qPCR thus far? Note: no PHE S dropout analysis for areas with low TaqPath coverage.

 

[elbows]

Looking just at death rates, quite a few European countries where things had been getting quite bad seem to have had quite a sudden drop-off in the past week or two, and it can be seen in the all-EU count too. Is that real or just an artefact of delayed reporting over Christmas I wonder?

On a somewhat related note: Credit where credit is due, the UKs testing system that started off so shit is now even able to put countries like Germany to shame when it comes to sustaining numbers of tests performed over the Christmas period.

 

[elbows]

Really depends on the specifics of the test(s) concerned.

AFAICS, all the (UK) literature on B.1.1.7 references data from Lighthouse (and affiliated labs) using the 3 channel Thermo Fisher TaqPath RT-qPCR thus far? Note: no PHE S dropout analysis for areas with low TaqPath coverage.

Indeed. I'd prefer it if such documents, when discussing the Lighthouse labs such as Milton Keynes that use TaqPath, bothered to discuss what systems were used elsewhere, and gave proper details about coverage of all systems, where the new variant blindspots are using the s-dropout proxy method.

I certainly hope that those labs that arent using the 3 channel TaqPath system are using systems that dont rely on S detection at all, as opposed to only relying on S detection.

 

[elbows]

Unless indicated otherwise I reckon its reasonable for me to stick to my prior assumption that tests which target S only are not part of the official test system. I dont have conclusive proof, but testing one area only would always be risky and bad for test reliability, and when I read things like the following from a Welsh document about the new variant, it all seems to point in the same direction as my assumption. My bold:

Some laboratories testing for presence of virus in people using Polymerase Chain Reaction (PCR) can also detect the variant through failure of one part of the test – this is due to a phenomenon called S-gene drop-out. S-gene dropout is due to one of the mutations in the VOC, a two codon deletion at positions 69 and 70 of the Spike protein. This mutation, not widely present in other SARS-CoV-2 variants circulating in the UK, causes diagnostic primers targeting this region of the spike protein to fail. To identify SARS CoV-2 infection a PCR test targets several parts of the viral genome, and some diagnostic tests include a target in the S-gene as one of several used in the test. Failure of the S-gene in a test does not mean the test will not identify people who are COVID-19 positive as other parts of the virus genome are still detected. Based upon the low frequency of other mutations in this area of the spike protein circulating in the UK, the S-gene drop-out provides a reasonable proxy method for detecting the new viral variant. Some but not all Lighthouse Laboratories (LHLs) use the test that can detect the variant. Other laboratories, including Public Health Wales (PHW), cannot detect the variant on the majority of their platforms.

From https://gov.wales/sites/default/fil...l-variant-voc-20201201-23-december-2020_0.pdf

 

[elbows]

I reckon its been a year since the first warning signs really started to show up on the english-speaking side of the internet:

Home - ProMED - ProMED-mail

ProMED is the largest publicly-available surveillance system conducting global reporting of infectious diseases outbreaks. Subscribe today.

promedmail.org

I used to read promed a lot years ago but I wasnt reading it a year ago so I didnt see that at the time. I'm not sure exactly when I heard about it first, probably early January, maybe via this sort of news story from January 3rd:

China pneumonia outbreak: Mystery virus probed in Wuhan

Some 44 people have been infected in the central city of Wuhan, officials say.

www.bbc.co.uk

 

[8ball]

I reckon its been a year since the first warning signs really started to show up on the english-speaking side of the internet:

I remember discussing it with my folks last December when I was home for Christmas and things were looking a bit worrying at that point.
I expect you were talking about it by then - might be worth a little search..

 

[teqniq]

WTF?

 

[platinumsage]

I reckon its been a year since the first warning signs really started to show up on the english-speaking side of the internet:

Home - ProMED - ProMED-mail

ProMED is the largest publicly-available surveillance system conducting global reporting of infectious diseases outbreaks. Subscribe today.

promedmail.org

I used to read promed a lot years ago but I wasnt reading it a year ago so I didnt see that at the time. I'm not sure exactly when I heard about it first, probably early January, maybe via this sort of news story from January 3rd:

China pneumonia outbreak: Mystery virus probed in Wuhan

Some 44 people have been infected in the central city of Wuhan, officials say.

www.bbc.co.uk

Hopefully when this happens again, a global travel ban from the originating country will be in place by the time an article such as that is published.

 

[frogwoman]

It's quite chilling reading articles like that now.

 

[elbows]

Hopefully when this happens again, a global travel ban from the originating country will be in place by the time an article such as that is published.

I would recommend such steps in order to reduce numbers. However I'm reasonably confident that it would still have been too late to stop the spread completely, the horse had bolted long before then in this pandemic, even if Wuhan was the original outbreak rather than simply being the first place where numbers grew high enough to be noticed.

Exhibit a:

A British man who died with coronavirus in his lungs in January is now believed to be the first virus fatality in the UK – two months earlier than previously thought. Peter Attwood, 84, died in hospital on January 30 after coming down with a cough and fever before Christmas. His initial cause of death was marked as heart failure and pneumonia. But tests carried out after his death revealed Covid-19 was present in his lung tissue, making him the UK’s earliest recorded death from the disease. Peter, a retired company secretary from Chatham, Kent, first had symptoms on December 15, two weeks before China told the World Health Organisation (WHO) about cases of ‘viral pneumonia’ in Wuhan.

Granddad's death shows Covid was in the UK 'much sooner than we've been told'

Peter Atwood started suffering symptoms in mid-December - a month before China told the world there was a problem.

metro.co.uk

 

[platinumsage]

I would recommend such steps in order to reduce numbers. However I'm reasonably confident that it would still have been too late to stop the spread completely, the horse had bolted long before then in this pandemic, even if Wuhan was the original outbreak rather than simply being the first place where numbers grew high enough to be noticed.

Exhibit a:

Granddad's death shows Covid was in the UK 'much sooner than we've been told'

Peter Atwood started suffering symptoms in mid-December - a month before China told the world there was a problem.

metro.co.uk

Sure, but I think it's obvious that extremely early and strict border controls would have given track and trace a much better chance of keeping total infection numbers within many countries in the tens or hundreds range rather than millions.

 

[elbows]

I remember discussing it with my folks last December when I was home for Christmas and things were looking a bit worrying at that point.
I expect you were talking about it by then - might be worth a little search..

I dont think the general public were discussing it until January. Mid January was the point where the penny really started to drop big time, and it was probably around then when I first thought 'oh dear, am I going to have to be the one to start a thread on this?'. But I didnt start a thread, and then it was only a few days later that weltweit started this one, and the rest is history.

 

[8ball]

I dont think the general public were discussing it until January. Mid January was the point where the penny really started to drop big time, and it was probably around then when I first thought 'oh dear, am I going to have to be the one to start a thread on this?'. But I didnt start a thread, and then it was only a few days later that weltweit started this one, and the rest is history.

I think it may have been continuing a theme from last Christmas where we were playing a bit of Pandemic and my nephews had Plague Inc. on their iPads come to think of it.

Somewhere in Jan, there was some talk of a "mystery pneumonia" (which I would have guessed was here, but I guess not if there was no thread) - then at some point in Feb it became clear that something really, really bad was happening and the Government seemed to sit on their hands for what felt like 3 weeks (might have been shorter, I was bloody enraged).

It's really hard to pinpoint the exact first time you heard about something when you've been hearing about little else for a year.

 

[frogwoman]

Just read on twitter that Peru may have a population fatality rate of 0.3%. or around 100,000 in a population of 33 million.

 

[Cloo]

Israel is apparently cracking on with vaccination at a tremendous rate, possibly due the extreme amount of loud complaint that will ensue if they don't.