Mutating Corona Virus

[brassnecked]

Test & Trace has been an unmitigated disaster except for the wallets of the people involved. Now its admitted PCR rubbish as it picks up any infection so gives false positive

 

something from The Lancet

 

https://www.thelancet.com/journals/lanres/article/PIIS2213-2600(20)30453-7/fulltext

 

Other take from Phillipines

 

https://www.manilatimes.net/2021/02/25/opinion/columnists/topanalysis/pcr-test-shortcomings-revealed-in-official-literature/845086/

[honeybee13]

So has the situation reversed, PCR is less reliable and LFTs are better?

 

There is more on how the £37bn is being spent on the BBC.

 

https://www.bbc.co.uk/news/amp/health-56340831

[honeybee13]

Article from the Byline Times about a tangled web of disinformation sites.

 

Nafeez Ahmed reveals how COVID pseudoscience and anti-lockdown groups have morphed into a sophisticated, well-funded global network

 

https://bylinetimes.com/2021/02/02/cambridge-analytica-psychologist-advising-global-covid-19-disinformation-network-linked-to-nigel-farage-and-conservative-party/

 

 

[tobyjugg2]

That manila times article is larger utter balderdash.

 

The issue with PCR is that it is nothing like the 95% accuracy it is spun as - just as the lateral flow is nowhere near as 'accurate as spun.

BUT they do give some indications of those with high viral loads - including some post infection 'false positives

Just as temperature checks at supermarkets, transport hubs would.

 

Otherwise it would just be symptomatic, and possibly just severely symptomatic people that would be found with others spreading the virus

 

We need to be careful with articles like that manilatimes one where they seem to allege that only people symptomatic with the illness are a threat when we know that many infectious carriers of the virus are pre post or none-symptomatic

 

 

That Handcock and sercos test and trace has been a very expensive sick joke since day one, and continues to be so seems without question.

[brassnecked]

Yes I put it up as examples of how its difficult sometimes to sort truth from fiction, but there are serious doubts about whether its about Public health or cash for cronies.

[tobyjugg2]

on a side note, I've been quite ill for 24 hours after the O/AZ vaccine yesterday morning

 

Like the middle part of a proper bout of flu

Nasty headaches, hot face cold hands and feet, muscle and joint pain

No arm soreness at injection site though Yaaayyy

 

Seems to be easing now.

[tobyjugg2]

Proposal:

We call it JHS test and trace

or JHHS if we think Dodo worth a mention - I dont

Edited March 11, 2021 by tobyjugg2

[tobyjugg2]

14 minutes ago, brassnecked said:

Yes I put it up as examples of how its difficult sometimes to sort truth from fiction, but there are serious doubts about whether its about Public health or cash for cronies.

 

None that I can see - I'm quite sure its about money for cronies

Even if JHS test and trace was just a pitiful 25% 'efficacious (sic) - 25 times its apparent actual effectiveness, I would think the same - although it would have been a little harder

[honeybee13]

I hope you feel better soon, TJ. Someone I know reacted to the vaccine but it calmed down pretty quickly.

[tobyjugg2]

Still getting some shivers and mild headache and feeling rather battered, but does seem to be fading albeit slower than it fired up.

Paracetamol+Ibuprofen  seems to mitigate symptoms VERY well.

 

Apparently, if it fades quickly its a sign of a young powerful immune system from what little I can find {smug} 

 

https://abc7news.com/covid-19-vaccine-reactions-moderna-vs-pfizer-what-are-the-side-effects-of/8805958/

https://inews.co.uk/news/health/covid-vaccine-side-effects-coronavirus-jab-minor-reactions-symptoms-explained-877533

Edited March 11, 2021 by tobyjugg2

[brassnecked]

EU still worried about AZ

https://www.dailymail.co.uk/news/article-9350283/Denmark-suspends-AstraZeneca-vaccine-effect-fears.html

[tobyjugg2]

so am I - and not necessarily side effects

I'd have had the pfiser any day of the week - and I tried

 

[BazzaS]

17 hours ago, tobyjugg2 said:

 

The issue with PCR is that it is nothing like the 95% accuracy it is spun as - just as the lateral flow is nowhere near as 'accurate as spun.

 

What do you mean by “nothing like the 95% accuracy”? how “accurate” is it?

 

by “accurate”, what do you mean? What specificity is the test?

What sensitivity,

what PPV?

What NPV?.

 

and which PCR (or PCR’s) are you referring to.

There are more than one, and some use different target sequences than others ........

 

I “dipped out” of the thread because you weren’t answering over the basis for your ‘facts’ on testing “accuracy”, but thought I’d take a look ....... so let’s see if anything has changed months later and if you can yet evidence understanding of sensitivity, specificity, PPV and NPV

(Hint : the PPV of lateral flow tests is a key issue behind

Covid-19: False test results 'ruining' return to school

https://www.bbc.co.uk/news/health-56349116    )

Edited March 12, 2021 by BazzaS

[honeybee13]

The DHSC are refusing to comply with a FoI request on the grounds that it would be inappropriate to spend £600 releasing details of meetings held by Dido Harding.

 

No problem with spending £37bn though.

 

https://www.huffingtonpost.co.uk/entry/test-and-trace-dido-harding-secret-meetings_uk_6049121cc5b672fce4ea0dcd

[tobyjugg2]

4 hours ago, BazzaS said:

 

What do you mean by “nothing like the 95% accuracy”? how “accurate” is it?

 

by “accurate”, what do you mean? What specificity is the test?

 

and which PCR (or PCR’s) are you referring to.

 

As there are a number as you state, to which are you asking specifics?

 

Care to name a PCR test in use that gives over 90% accuracy outside of laboratories across the spectrum of levels of infection and viral load?

and If you do, and as as far as I am aware you dont get a choice what you get, have do you know? aka prove it.

[tobyjugg2]

Clarification

Laboritory test above means the actual laboritory tests performed to test the effectiveness - not PCR tests bulk returned from mass test sites

 

Lateral flow tests are of course notoriously inaccurate as they have to work from a 'calculated 'norm'

[tobyjugg2]

Of course if you look at"unrepentant and inveterate liar" johnson approved reports, the claims are much higher ..

but only a fool would believe those.

 

take a look at the FDA's figures (so no-one can claim its the EU so they are lying)

https://www.fda.gov/medical-devices/coronavirus-disease-2019-covid-19-emergency-use-authorizations-medical-devices/vitro-diagnostics-euas

 

Those are largely laboratory test results

Real world tests, few as they are, give FAAAAR lower ratings

Its interesting that false negative are easier to get actual real world figures on

 

eg

""What about accuracy? The rate of false negatives — a test that says you don’t have the virus when you actually do have the virus — varies depending on how long infection has been present: in one study, the false-negative rate was 20% when testing was performed five days after symptoms began, but much higher (up to 100%) earlier in infection.

-FDA

[BazzaS]

5 hours ago, tobyjugg2 said:

 

As there are a number as you state, to which are you asking specifics?

 

Care to name a PCR test in use that gives over 90% accuracy outside of laboratories across the spectrum of levels of infection and viral load?

and If you do, and as as far as I am aware you dont get a choice what you get, have do you know? aka prove it.

I’m asking you to give those specifics (since you “quote” figures but never back them up as to sensitivity/ specificity, +ve and negative PV’s). I don’t know which tests to ask you about, because you haven’t said which tests you are giving figures for!

 

”name a PCR test in use that gives over 90% accuracy outside of labs”

it depends what you mean by “labs”, and “accuracy”, and for that matter “PCR”

 

Accuracy : see above. Do you mean sensitivity/ specificity (and which?), or PPV / NPV? (and which!), or threshold of detection of the assay?

“outside of labs”

that’s a difficult task, since most PCR’s are done in labs, it’s pretty hard to name one in use outside of labs!

However, 

there is “point of care testing” such as the SAMBA2 system, which some hospitals still use in a lab setting, and some in a more front-line POCT manner.

Strictly speaking it is a NAAT rather than a PCR (PCR is Roche’s trademark, with Nucleic Acid Amplification Test being the more generic term. Think “Hoover” and “vacuum cleaner”.

all Hoover vacuums are vacuum, not all vacuum are Hoover, all PCR’s are NAATs, not all NAATs are PCR’s .....)

 

limit of detection? 100% at 250 copies/ml

66.7 % at 150 copies /ml, but nil at 100 copies / ml.

sensitivity/ specificity varies by which trial you cite. A study at CUH (Addenbrooke’s) gave sensitivity of 97% and specificity 100%.
I have the CI’s stated if you need ......

 

for a NAAT done “in labs”, for the Viasure kit (for ‘Covid’ alone, not the multiplex that includes other respiratory viruses as well as SARS-nCoV- 2), the manufacturer quotes a study from Spain with sensitivity > 99%, specificity > 99%.

 

For the multiplex Viasure , for SARS-nCoV-2 the manufacturer quotes a comparison with other test kits, rather than with cell culture, so they don’t quote e.g.sensitivity but instead PPA of 94.7%, NPA of 100%, and OPA 98.7 % (again, I have the CI’s if you’d like).

 

How do I know? By checking the manufacture’s data sheets ....

 

can I check myself (“aka prove it”):

Sadly I don’t have the facilities (and Hazard Group licensing of them) to do SARS-nCoV-2 tissue culture to check (the sensitivity/ specificity / threshold of detection of the assay) myself. If you really need, phone Porton and ask : they’ve done so for most of the commercial PCR’s......

if (for a given sensitivity/ specificity) you want the PPV and NPV, you’ll need to give me one key piece of data to derive them, without which : can’t be done.

 

All of these are also operator dependant ‘in the real world. If the sample is poorly taken, less sensitivity.

they are also site / sample dependant. Viral replication takes place in the nasopharynx early on, but nasopharyngeal samples can be negative later in the disease, and if ‘Covid pneumonitis’ is a concern, deep respiratory samples would be preferable (“more accurate”, to use the imprecise terminology you’ve used) compared with nasopharyngeal.

 

Now I’ve answered (within the realistic limits I’ve explained) : how about you answer (currently, and for ALL the times I’ve asked previously!) for the figures you’ve been stating.....

[BazzaS]

7 hours ago, tobyjugg2 said:

Clarification

Laboritory test above means the actual laboritory tests performed to test the effectiveness - not PCR tests bulk returned from mass test sites

 

Lateral flow tests are of course notoriously inaccurate as they have to work from a 'calculated 'norm'

do you mean sensitivity / specificity studies?

the kit manufacturers publish their data.

Porton (though I’m not sure “which side of the fence”) did some validation studies of their own comparing kits early on ......

[tobyjugg2]

bit rich from one who asks a question, part of which defines it as meaningless, then goes on to accuse others

 

what do I mean by 90% accuracy?

That none of the tests applied, in any situation gives a result that goes below 90%

 

eg If any PCR test gives less than 90% accuracy in either positive or negative infection state from a truely random or selected wide spread of genetic/infection levels

Not that it can manage 97% of catching pre tested high viral load samples

 while struggling to hit 70% for accurately identifying negative infection in confirmed non infection samples.

 

Of course the definitions of what covid infection or not are is changing almost by the day.

 

 

Rather than Bazzas blown up Baloney

Heres a far more straightforward and honest assessment of the LFT 'gold standard test' claimed at "99.6% specificity and high sensitivity compared to PCR" by "unrepentant and inveterate liar" Johnsons lackies

 

The truth:

https://www.bmj.com/content/371/bmj.m4469

 

summary

"Sensitivity dropped to 73% when used by trained healthcare staff (92/126 positive: 73.0% (64.3% to 80.5%))

and to 58% with self-trained members of the public (214/372 positive: 57.5% (52.3% to 62.6%))."

 

"while 0.4% (400 in 100 000) was a very low rate, with a sensitivity of 58% and specificity of 99.6%, this would mean that 100 000 people being tested would find 630 positives—of which only 230 would actually have covid-19, while 400 would be false positives.

“The poor detection rate of the test makes it entirely unsuitable for the government’s claim that it will allow safe ‘test and release’ of people from lockdown and students from university,”

 

 

and although the specific example is LFT - the same techniques and selective carefully chosen extracts are used in PCR claims by the dishonest, with anything that might 'put an accurate shade on it carefully omitted.

 

Edited March 12, 2021 by tobyjugg2

[BazzaS]

You were asking about PCR’s.

I answered about PCR’s / NAATs.

now your bluster about PCR’s has been exposed you pull out the BMJ paper in an attempt at misdirection.

That BMJ paper refers to LFT’s, which aren’t NAATs (let alone PCR).......

 

 

you still can’t explain what you mean by “accuracy”, and have shown no evidence of understanding sensitivity / specificity and their application to give PPV and NPV.

 

your comment of
“eg If any PCR test gives less than 90% accuracy in either positive or negative infection state from a truely random or selected wide spread of genetic/infection levels” is meaningless. It is pseudo-scientific babble.

This is why I’m trying to pin you down to if you mean sensitivity/ specificity (lab defined values which shouldn’t change much : just slightly different results by sample variation in different studies) or the more real world PPV/NPV, which can vary massively depending on a real world variable. (Care to say the one word that influences this??)

 

“Not that it can manage 97% of catching pre tested high viral load samples

 while struggling to hit 70% for accurately identifying negative infection in confirmed non infection samples.” 

At least approaches some meaning, but the NAAT I’ve highlighted exceeds 97% sensitivity for positives (not just those with high copies/ml), and exceeds 70% specificity for negatives .....

 

moving to the LFT’s you’ve tried to introduce to muddy the waters of being called out over the PCRs:

 

Lateral flow tests are far from a gold standard.

I’ve never said otherwise.

They have advantages that mean they have their place, but need an understanding of their limitations ... precisely of their NPV and PPV, and the human ‘cost’ of a false positive (and false negative too!).

 

As I say, sensitivity, specificity, PPV and NPV are all defined measures of test “accuracy”.

If you try talking about “accuracy” without understanding them and knowing what you mean, you can’t expect those who do know what they mean to be convinced by you quoting papers at random when you are misapplying them.

Edited March 12, 2021 by BazzaS

[tobyjugg2]

 

1 hour ago, BazzaS said:

That BMJ paper refers to LFT’s,

 

 

2 hours ago, tobyjugg2 said:

the LFT 'gold standard test' 

 

Quote

and although the specific example is LFT - the same techniques and selective carefully chosen extracts are used in PCR claims by the dishonest, with anything that might 'put an accurate shade on it carefully omitted.

 

 

yes I did quite clearly state that - twice

and the calculations for accuracy, or sensitivity/specificity if you want to use the jargon are the same

it was just that that article was nice and clear and wasn't filled with waffling jargon intended to hides facts - or lack of actual understanding.

 

You are completely avoiding (trying to) the simple fact that the claims of 95% or 97% as innova claimed

are in very specific circumstances - ie when testing already tested positives with specific high viral loads

.. and still ONLY show part of the picture at that

 

All it really shows is that the test misses 3 out of a hundred people with high viral loads who have already tested positive

Want to carry on disputing that?

 

I'm not disputing they are still useful (pcr or lft) - they absolutely are - but the presented information should be honest open and clear and used appropriately - not misrepresented choice pieces and used based on the misrepresentations.

 

 

The BMJ article I linked presents real world results compared to ideal condition limited subject claims quite clearly IMO

 

"The evaluation found that the test performed best when used by laboratory scientists when the sensitivity was 79% (156/197 positive: 79.2% (95% confidence interval 72.8% to 84.6%))."

 

2 hours ago, tobyjugg2 said:

 

"Sensitivity dropped to 73% when used by trained healthcare staff (92/126 positive: 73.0% (64.3% to 80.5%))

and to 58% with self-trained members of the public (214/372 positive: 57.5% (52.3% to 62.6%))."

 

"while 0.4% (400 in 100 000) was a very low rate, with a sensitivity of 58% and specificity of 99.6%, this would mean that 100 000 people being tested would find 630 positives—of which only 230 would actually have covid-19, while 400 would be false positives.

“The poor detection rate of the test makes it entirely unsuitable for the government’s claim that it will allow safe ‘test and release’ of people from lockdown and students from university,”

 

 

 

An excellent example of how LFT and PCR are (mis)presented

 

Edited March 12, 2021 by tobyjugg2

[BazzaS]

Back to the Innova Lateral flow test by you.

 

Look back : you asked about “PCR”, I answered about PCR (and other NAATs).

So, why do you keep introducing lateral flow tests? As a misdirection because I actually answered about PCR’s, and you gave no sensible reply to those details?

As for me wanting to use the “jargon” of sensitivity / specificity - of course I want to use “the jargon”. If I hadn’t you’d have been accusing me of not citing facts. When I cite facts you say it is jargon. Make up your mind!.

 

Of course the ideal would be a 100 % sensitive, 100% specific test. Since sensitivity and specificity are by comparison with “the gold standard”, by definition, that is the gold standard (or a comparable, new, gold standard that might be easier / cheaper / quicker than, say, cell culture ........)

 

no PCR (yet!) is 100% sensitive and 100% specific.

Because you haven’t been able to name the missing variable to derive NPV and PPV, the one word I was looking for is “prevalence”.

 

So, let me know what you consider an “accurate” test in terms of both sensitivity and specificity. If you’d like give me rates for number of true +ve, number of true negative, and the corresponding numbers of false +Ve’s and false negatives for (say) 100 tests, then

I’ll give you the sensitivity, specificity, NPV, PPV and prevalence.

 

Or you can give me sensitivity and specificity, together with the prevalence, and I’ll give you the NPV and PPV.

 

Surely that isn’t too hard? Even better if you use the details (sensitivity/ specificity)  for a real world test and current (or recent) prevalence .... maybe the data from REACT?

 

That way we can talk about “accuracy” that reflects the real world.............

but, if you prefer to use a made up sensitivity, specificity and prevalence.... it should still be instructive

 

Edited March 12, 2021 by BazzaS

[tobyjugg2]

10 hours ago, BazzaS said:

Blah blah

 

Ok so you dont like my deliberately de-jargonised terminology. I dont care. I de-jargonise deliberately.

 

So what is your actual issue/critique with the BMJ article?

 

 

[BazzaS]

2 hours ago, tobyjugg2 said:

 

Ok so you dont like my deliberately de-jargonised terminology. I dont care. I de-jargonise deliberately.

 

Or because you don’t understand.

 

When a company asks me “should we use this test?” I take them through 3 (sometimes more) steps to get them to understand “accuracy”, and the implications of which test they might use, and (just as importantly, it’s implications, both now, and in the future .....)

 

1. Sensitivity / Specificity. (In terms of why scientists produce these for the tests, and what they mean, but then ........)

2. Why sensitivity/ specificity mean NOTHING to the average person who gets a result (“+ve” or “-ve”), and what they mean, (by using PPV and NPV)

3. A further step regarding NPV / PPV.

 

This suits for most queries. Very occasionally they want more depth, but not many need / want to consider:

4. ROC plots  and sensitivity / specificity trade-off in test development .......

However, you can’t seem to achieve (let alone get past) Step 1.

 

Quote

 

So what is your actual issue/critique with the BMJ article?

 

 

 

No critique of the BMJ article. The author clearly understands steps 1-3 (and probably step 4+, but again, Steps 4+ isn’t what most people need to consider......which is likely why they haven’t ‘gone past’ Step 3).

 

I repeat (since I’ve said it before) that BMJ article discusses the Innova LFT. You wanted “accuracy” figures for “PCR outside of labs”.

 

I’ve explained, given you sensitivity and specificity figures for a NAAT “outside of a lab”, and a PCR “in a lab”.

 

To distract from you not being able to accept you’ve had your query answered, and you can’t answer about the sensitivity and specificity of a PCR (which is what you were asking about!), you’ve tried to divert attention to a lateral flow test.

 

So, my issue isn’t with the BMJ article, but instead with you using that article to conflate PCR’s / NAATs with LFTs (likely because you can’t accept your comments on PCR sensitivity/ specificity were wrong, you can’t accept I answered your question, and you “de-jargonise deliberately” because you’ve shown you can’t understand / move past step 1) ........ 

 

It’s akin to you insisting on answers about apples, and then when you don’t like the answer, and can’t explain your statements about apples, bringing in oranges to the discussion (they are all fruits, right?) in the hope you can distract attention from the discussion on apples.

Edited March 13, 2021 by BazzaS