Covid 19

[maxf]

So now maxf attempts the well worn technique of the "Gish Gallop".https://en.wikipedia.org/wiki/Gish_gallop but brings no new arguments.

Others have dealt with the false positives (again, read up on Bayes Theorem), LPF sensitivity (again), changes in reporting criteria obviously alter figures, and as for the "Great Barrington Declaration!

The instigators of the GBD are the very people who declared the epidemic over in June, that herd immunity has been obtained, claimed that there would be no second wave etc. etc.  They have been repeatedly shown by events to be wrong.  Quoting the number of signatories isn't wise when they include multiple Drs Harold Shipman and other notable medics.

The GBD argues for shielding the vulnerable, which is unfeasible as has been explained many times. Society doesn't come in nice isolated groups you can divide.  It also ignores the large number of people incapacitated and people surviving with long term organ damage, including strokes.

Letting a virus spread unchecked has other dangers including increasing the likelihood of more dangerous mutations, as has occurred. There is now very strong evidence that it is increasingly infectious and in the younger age groups ( < 20 years old). Intensivists are reporting more younger patients and hospitals in London and the SE are now sending critically ill patients to distant hospitals because they have exceeded their ITU capacity.

You are repeating the same points that have already been dealt with but you have ignored the responses.

It is obvious you aren't discussing things in good faith so what is your agenda? Or are you just a Sea Lion? https://en.wikipedia.org/wiki/Sealioning

Please do something constructive like point me in the direction of some sort of approval tests for which PCR, LFT and lab cultures have all been tested and compared against then for the same patients.

 

[maxf]

Here is some further evidence that incorrect use of PCR testing can give rise to false positives.

https://t.co/t4qQN4rH0u?amp=1

Source, Royal College of Physicians...

 

[andrewmcleod]

Here is some further evidence that incorrect use of PCR testing can give rise to false positives.

https://t.co/t4qQN4rH0u?amp=1

Source, Royal College of Physicians...

https://en.wikipedia.org/wiki/Not_even_wrong

The most disappointing thing about arguing in favour of positions supported by the mainstream of science against those positions that are not supported by the science is that the proponents of unscientific viewpoints think that the 'facts' are the issue, as if single throw-away pieces of opinion or evidence could destroy the entire edifice of science. They seem to think that a well-placed hammer blow of 'ah, but' will bring the tower crumbling down. What they don't see is that as they swing their nutcracker against the vast construction of knowledge, a thousand scientists swing mighty sledgehammers against the tower, trying to knock it down as quickly as others build it. Yet it grows, nonetheless - not a lofty tower or elegant cathedral, but more like a nuclear bunker of robust concrete. Always there are errors, parts which do not fit which must be destroyed so that better-fitting (yet still incorrect) parts may take their place.

Sometimes people seem to think the default position of scientists is certainty, of knowledge in facts. This is wrong - the default state of scientists is doubt, and at the coal face of their field, ignorance. Science is built on trust, because no one person can know all that is needed. But that trust is earned, not given freely. So when a scientist says a thing is so, rarely they will say it because they (and sometimes they alone) are a person who has spent years studying it - and will still (usually) admit they could be wrong. More often they say it because they trust those who have studied it have done so in a robust manner that has been checked by others (it is much easier to verify another's work than to get there in the first place).

Find me a single serious scientist who doesn't believe that PCR tests, or any diagnostic tests, are completely without error. When the PCR tests for Covid were first developed, the error rates were stated alongside (even in the news). Do you think scientists simply trusted that? A part of science is to critique the work of others, to destroy what others has created - only the strongest theories, the best-supported evidence will survive. The stated error rates are, of course, in perfect use and cannot account for accidents, contamination etc.

Indeed, even in this very thread, people have explained the (very) basic statistics behind how, in a population where the incidence of a disease is low, most positive test cases will be false positives even if the false positive rate is very low. For example, a significant fraction (most?) people who test positive for HIV do not have HIV - despite the very low false positive rate of the tests. This is not complicated. This isn't even epidemiology 101; this is trivial.

So when you give a quote that tests have a false positive, it displays a total lack of appreciation of the problem at hand. How could you even think that matters? Every scientist working with Covid will know these tests have false positive and negative rates. Every scientist knows the LFTs are crap (although many will have a detailed understanding of exactly how crap, allowing them to still be useful in the right circumstances). What are you even trying do achieve here? Do you even know what a PCR test is, what the acronym stands for, how it is carried out? What value have you added to this debate, beyond regurgitating cherry-picked stuff from the web?

Finally, why do you think you know better? I don't; I have a PhD in Astrophysics and that gives me a lot of scientific skills. It tells me bugger all about immunology or epidemiology. I trust in the science, not blindly, not in faith, but knowing that trust has been earned.

 

[Speleofish]

Beautifully put. Much better than I would have done.

 

[aardgoose]

Please do something constructive like point me in the direction of some sort of approval tests for which PCR, LFT and lab cultures have all been tested and compared against then for the same patients.

If you were interested in facts you could have easily found out the following information.  That you continue to dispute well evidenced facts confirms that you are invested in disbelieving not learning.

But to humour you:

You can find some of the procedures for use and documented testing regime for one the main PCR tests used in the UK. You might be pleased to notice that the operational procedures also include known test samples to ensure accurate use. It also documents the testing of the kits for use.

I am afraid I can't point you to tests against the same patient, because that isn't how the approval process works.  They use standardised samples of known virus concentration produced in controlled conditions, a method that can be used internationally and reliably.

PCR isn't a new technique. It was invented in 1985.

https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0019215_TaqPathCOVID-19_CE-IVD_RT-PCR%20Kit_IFU.pdf

The following paper's abstract discusses the known limitations of Lateral Flow tests (aka LFA), but a standout sentence from it is:

However, the inability to detect the early onset of COVID-19 means serology LFAs are not considered useful for case detection or diagnosis of SARS-CoV-2 infection, for the purposes of treatment or isolation.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7409939/

Also:

Covid-19: Lateral flow tests miss over half of cases, Liverpool pilot data show

https://www.bmj.com/content/371/bmj.m4848

The characteristics of the two test types are well established.

In addition to this, the UK sequencing program where a significant proportion of positive samples from the testing labs are fully sequenced further demonstrates that the PCR test results are accurate.  A significant false positive rate would have been detected at that stage. Over 100,000 samples have been sequenced in this way.

 

[alastairgott]

105 posts in 5 days... that's an average proliferation of 21 posts per day, i'd say this thread is infectious.

 

[NewStuff]

105 posts in 5 days... that's an average proliferation of 21 posts per day, i'd say this thread is infectious.

It's still not as fun as, say, a good old CRoW thread. 

 

[ZombieCake]

105 posts in 5 days... that's an average proliferation of 21 posts per day, i'd say this thread is infectious.

Is 'And-another-thing-rage-rant-itis' very contagious?  I guess most have had it at one time or another. 

 

[Badlad]

I'm happy to take the vaccine at any time - sooner the better.  I've taken all sorts of jabs in my time, all the childhood immunisations and loads of inoculations for travel.  I've no worries on that front.

I'm not too worried about covid19 from a personal point of view.  If I get it I reckon I have a very high chance of survival but i do recognise the danger the disease poses to many different people and the effect the illness has on the struggling NHS.

What does concern me is the way the whole pandemic has been handled by government.  Everything from running down of local community response services over the years, to centralisation and the dodgy contracts to mates, the Cummings effect and allowing the rich and powerful to bend the rules as they like and, mostly, the plain god dam awful leadership of Boris 'the U turn' Johnson. 

I'm not much of a Guardian reader normally, nor any other newspaper for that matter, but I did find this opinion interesting.  So in the spirit of everyone posting links to make a point

https://www.theguardian.com/commentisfree/2021/jan/02/follow-covid-restrictions-break-rules-compliance

:ang:

 

[PeteHall]

Totally agree Badlad.

Likewise I'll take the vaccine when I'm offered it (assuming some previously unrecorded and catastrophic side effects don't come to light in the meantime, which there is little reason to expect).

Likewise, I'm not too worried about my personal risk of Covid, but I appreciate that precautions are sensible to protect those who are more vulnerable.

Likewise, my biggest concern is the way that the UK government (and devolved powers) have handled the situation.

To pick up on andrewmc's earlier point about scientists understanding false positive/ negative test results, I don't doubt that for a  minute, but unfortunately the same cannot be said for our politicians, who are making the decisions. Very often their choices seem to focus on political point scoring and to trying to defend their previous bad decisions, rather than being led by the science, as they claim. There is a complete lack of honesty and transparency from the government and that is reciprocated by a complete lack of trust from large portions of the public.

Our politicians seem to have a very poor grasp of basic statistics, (as in the mathematical science of interpreting the numbers, not necessarily the numbers themselves), in fact, I heard an interesting interview with a psychologist a while ago explaining that human beings in general are very bad at statistics. So when a politician quotes a load of statistics and predictions that they don't understand, to a public that doesn't understand and then implements a policy based on a politically motivated catchphrase off the back of this, it's no surprise that there is such a shitstorm.

 

[droid]

I'm genuinely open minded about it but have yet to have some of the 'tin foil bridges' points proven to me otherwise...

No you aren't.

Or your knowledge of Biology is, to put it politely, shite....

 

[crickleymal]

I had covid,  my family had it too, back in April and I was lucky not to end up in hospital.  Fortunately I was prescribed some steroids which kept me going. However my best friend died of covid in November.  His wife had a stroke and was diagnosed covid positive but asymptomatic.  He may well have caught it off her and was ok with a slight cold on a Tuesday,  in hospital on Thursday and dead on Saturday.

His wife has to cope with that.

We saw it coming and decided to stockpile food in January so it didn't hit us too hard.

 

[maxf]

Please study tables 6a and 6b, you will note up to 45% of positive tests are being accepted in some regional areas on single gene positivey only....

https://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/datasets/coronaviruscovid19infectionsurveydata

If you dont believe this information in the above link coupled with this information below:

https://t.co/t4qQN4rH0u?amp=1

Is significant in showing that there could be a much higher positive test rate than actual person with corona infection rate then i would highly question any scientific skills you believe you might have

 

[mikem]

Doesn't really matter because decisions are being made on ICU beds available & comparative rates, not total numbers.

The 2nd link is a download.

 

[andrewmcleod]

Is significant in showing that there could be a much higher positive test rate than actual person with corona infection rate then i would highly question any scientific skills you believe you might have

What scientific skills do you have, which would give you some basis to criticise the scientific skills of others? I've published in peer-reviewed journals - it's bloody hard work (in the proper ones). You just wouldn't get away with imprecise, vague and unsupported assertions such as yours. 'could be a much higher' - much higher than what? How much higher? What's your evidence? You've not given an argument, just a few links and an unargued claim. You shouldn't even get away with that at undergrad level (at a decent mark, anyway).

The first link says, at the bottom, '2. Swabs are tested for 3 genes present in the coronavirus: N protein, S protein and ORF1ab. Each swab can have any one, any two or all three genes detected. Positives are those where one or more of these genes is detected in the swab other than tests that are only positive on the S-gene which is not considered a reliable indicator of the virus if found on its own.'
That (implicitly) claims that a single N protein or ORF1ab result is considered a reliable indicator of the virus if found on its own. The burden of proof is on you to demonstrate otherwise.

In response to "Please study tables 6a and 6b, you will note up to 45% of positive tests are being accepted in some regional areas on single gene positivey only....", so what?

You are trying to use your second link as evidence of 'bad things' but actually its proof of science working. Here is a real scientist, who actually knows what he is talking about (or at least can do a good pretence), pointing out the limitations of these things. Other scientists will read this (in fact are far more likely to read it than the social media crowd, since that is their job) and agree/disagree in an informed way. Then science will move forwards. In fact (having had a flick through) nothing in that paper will be even remotely surprising to anyone in the field - what do you think is significant?

If your argument doesn't have actual numbers in, then it's just waffle - this is not a yes/no thing, but a 'is this thing that we know about significant or not'. Given that the people doing this analysis are grown-ups who actually know what they are doing, why do you think they are doing it wrong, and why would you know better?

Just out of curiosity, what is your academic education?

Here's some questions for you, if you really have any idea what you are talking about:

What was the false positive rate in the Healy et al study? (2 marks)

Why are so many of the positive tests in the Healy et al study false positives? (5 marks)

Why will this currently be less of an issue (in some ways)? (2 marks)

 

[andrewmcleod]

Extra fun fact: the reported positivity rate for England over the summer was around 0.05% to 0.1% (from the ONS COVID-19 Infection Study), much lower than that reporting in the Healy et al study, which suggests the false positive percentage is also much smaller. I don't know why; possibly their criteria are more stringent or the genes they are matching are more reliable.

Current positivity rates are more like 1.25% or so. There's no reason to think the false positive percentage will have changed.

 

[PeteHall]

The first link says, at the bottom, '2. Swabs are tested for 3 genes present in the coronavirus: N protein, S protein and ORF1ab. Each swab can have any one, any two or all three genes detected. Positives are those where one or more of these genes is detected in the swab other than tests that are only positive on the S-gene which is not considered a reliable indicator of the virus if found on its own.'
That (implicitly) claims that a single N protein or ORF1ab result is considered a reliable indicator of the virus if found on its own. The burden of proof is on you to demonstrate otherwise.

The 2nd link (Royal College of Physicians, Healy et al study) states that "Our results show that 26/31 were positive at low level (Ct>35) in a single gene, which is considered as a likely false positive result."

Clearly there is some discrepancy in the interpretation of what is or is not considered a likely false positive result. Both make an assertion about what is 'considered' a reliable result, though neither specifically reference where that consideration has come from.

If you were to go with the Healy et al assertion that a single gene positive was a likely false positive, then a proportion of the data in the ONS Infection Survey is likely to be false positive.

 

[maxf]

In addition to this, the UK sequencing program where a significant proportion of positive samples from the testing labs are fully sequenced further demonstrates that the PCR test results are accurate.  A significant false positive rate would have been detected at that stage. Over 100,000 samples have been sequenced in this way.

https://www.cogconsortium.uk/news_item/update-on-new-sars-cov-2-variant-and-how-cog-uk-tracks-emerging-mutations/

By their own admission they have only sequenced 10% of positive tests so by no means enough to say any significant false positive rate could be detected as you imply.

 

[andrewmcleod]

If you were to go with the Healy et al assertion that a single gene positive was a likely false positive, then a proportion of the data in the ONS Infection Survey is likely to be false positive.

I mean the fact that some fraction of the results in any such study are false positives is almost certainly true. The question is - what percentage, does it matter, and when does it matter.
The Healy study used different genes and may have used different methodologies, and so will have different false positive percentages.
Given that the positivity rates during times of low prevalence were as low as 0.05% to 0.1% in the ONS study, the false positive percentage (which remains effectively constant when the prevalence is lowish, and will decrease as prevalence approaches 100%) CANNOT be more than 0.05% to 0.1%.

 

[andrewmcleod]

https://www.cogconsortium.uk/news_item/update-on-new-sars-cov-2-variant-and-how-cog-uk-tracks-emerging-mutations/

By their own admission they have only sequenced 10% of positive tests so by no means enough to say any significant false positive rate could be detected as you imply.

Why?

Suppose you have 100,000 positive test results. 200 are false positives (0.2% false positive rate)
If you randomly sample 10% of that, that's 10,000 tests, of which 20 will be false positives.
You detect the 20 false positives. You calculate a false positive percentage of 100 * 20 / 10000 = 0.2%.
Job done. What's the problem?

Also - I dare you to try and answer my questions. Some of them are literally just reading comprehension. If you think you have any idea at all what you are talking about, they should be easy.

I double dare you.