If you haven’t seen all the chatter that states PCRs using more than thirty-something (someone even suggested 25 to me!) cycles will suffer from false positives, and so are useless, then read no further. For those who have seen this and wondered, I have two bits of data to show top highlight why the false-positive PCR problem is not a problem at all for SARS-CoV-2 diagnostics. And then there’s a rant.
False positives are really uncommon in practice
Below I’ve included an RT-PCR ‘run’ performed some years ago. It was screening nucleic acids extracted from sick human respiratory swabs and aspirates, looking for human parainfluenza virus type 4 (HPIV-4).
The RT-PCR was run for 55 cycles. Not 30. Not 40. Not 45. 55.
That’s excessive, but I actually liked to do that in my research days to a) make sure the test wasn’t doing anything weird and b) that there weren’t really weak positives I was missing (if a sample came up late (never saw one above 45) I would use a suite of other PCR tests to investigate further.
The point is that after 55 cycles of amplifying nucleic extracts from human respiratory tract samples, the only thing that crossed the threshold (red line in the figure below) was the positive control (a known extract of HPIV-4 RNA). I have the same sort of data for other viruses.
To say that any PCR run for more than thirty-something cycles will be a false positive or increase the likelihood of a false positive is misleading and wrong. The false-positive PCR problem is not a problem.
Thirty-something and biological variability
Look, I fully agree that the later (higher the numerical value) the threshold cycle (CT “cycle number”) of the RT-PCR result, the less target RNA is present at the start of the reaction. That RNA is a surrogate marker for the amount of virus but not an actual measure because PCR methods can’t tell you a virus is infectious.
By the way, people are very chuffed to have learned this fact in 2020. You can tell because they say so—a lot. But despite their newfound out-of-context knowledge, they actually know very little about what they’re talking about.
NOTE: while successful detection of viral RNA or DNA doesn’t guarantee the presence of culturable virus, please don’t be so silly as to suggest it must then mean there isn’t any infectious virus present, as someone just did on Twitter. Let’s make a bold call – a positive PCR detection means infectious virus is usually present. And if not at the time of sampling, it was only hours or days ago. You are infected by that virus and that virus is a thing not normally in your body. This is a new and important result at a time when the world is trying to reduce virus transmission – which it can’t do unless it knows where it is.
Most of the time, if you pick two different labs to test a panel of the same samples, you’ll get two sets of subtly (sometimes not so subtly) different results. Molecular biology people each have their favoured way of doing things and they get quite dogged in their ways.🙄
A single CT isn’t comparable
I’ve lifted a figure from an article. It highlights this variability, which definitely also extends into the much more volatile realm of cell culture and virus isolation (growing virus from a patient’s sample using immortal cell preparations grown in flasks).
The figure shows that if you were to blindly and ignorantly rely on single CT values to proclaim a lack of infectious risk – let’s say 35 or greater – you would miss people who were still shedding infectious virus.
If you surveyed more labs with expertise in cell culture and virus isolation and labs that could get hold of fresh samples and samples from the actual site of virus replication, I’m sure you could find even later CTs. You can also find labs that can’t isolate viruses from samples with CTs this late. This biological variability means we need to step back from these stupid single-number cut-offs.
Ummmmm…what false positives?
When presented with a conspiracy theory, I like to ask for the evidence. I generally reject YouTube video sources and weird websites. They never have facts, just beliefs and opinions.
So the real question is: where, oh theorists of the conspiracy type, are all these false positives that lots of PCRs all over the world are generating?
(h/t to Klaus Hentrich for this idea)
Let’s look at Australia.
We have no reported local transmission of SARS-CoV-2 or cases of COVID-19 disease to speak of as I write this. I reckon that’s a pretty low prevalence in a country of 25 million.
Australia’s COVID-19 cases right now are almost exclusively in quarantine hotels and among Aussies returning, or special-purpose travellers visiting, from a world on fire. We’ve had a few clusters
This has only been managed in a handful of locations. Specifically, Wuhan (and China in general, which peaked at around 4,000 daily cases)[6] and Singapore, which contained a dormitory outbreak that peaked at 1,400 cases per day as well as more widespread community cases (outside that crowded foreign worker dorm environment) which never reached higher than 50 cases per day.[5] Both of these locations have now had multiple doughnut days (or months).
Australia hasn’t seen its combined national daily tally of almost exclusively PCR-based tests fall below 20,000 since June. By the way, these aren’t just test results from hotel quarantine—they are mostly from among the community in each of Australia’s eight jurisdictions.
Source: the excellent ABC News website.[2]
All that testing provides a good number of opportunities for those so-called false-positive PCR results to show up in our daily reported numbers. Surely more testing should mean a steady flow of false positives if these conspiracies are correct? Others love to add that it should be even more of a problem in a low-prevalence setting. Australia certainly fits that bill. Plus, we’re testing mostly sick people but also asymptomatic and presymptomatic people.
But lo and behold, there is no steady stream of false positives. We don’t have an issue because, once again, this is an over-oxygenated amateur conspiracy theory and not an actual issue.
If we have a look at the next figure, we can see no constant stream of positives among the local testing. Yes, cases are occurring (as far as I know, mostly the same RT-PCR-based testing) among those coming from outside Australia but these are – as far as I know – linked to ill travellers diagnosed as having COVID-19. Actual clinical cases. The false-positive PCR problem is not a problem.
That’s not to say there are never false positives. There are. But they are very, very rare events that are almost always caught by the process involved in reporting test results. This process considers the lab results alongside clinical and epidemiological context and checks itself before reporting.
It may be that some parts of the world are too overwhelmed to use that sort that process. And in that instance, other testing might prove helpful. For example the less sensitive overall, but contagiousness-detecting rapid antigen tests may be helpful.[4] Or they might not; there isn’t a lot of real-world evidence for or against their helpfulness. But in the US – what is there to lose?
Nonetheless, an overwhelmed testing system doesn’t make PCR results useless it just makes them less obtainable.
The false-positive PCR problem is not a problem
There clearly isn’t a CT crisis or a false positive plague or a “casedemic”. The false-positive PCR problem is not a problem. There is, however, a crisis in the lack of understanding about a heretofore obscure branch of science that toils in relative obscurity and a tool it relies on; pathology testing and PCR.
But hey, is anyone actually saying there is a problem? Sadly, yes. These are is a couple of the many I’ve read. One is a comment currently in holding, submitted to this blog. The other a tweet at me last night. And yet despite sounding so sure of itself, it isn’t supported by facts and is simply absolute rubbish.
Don’t blame PCR for lots of positive people – blame your government
Just about every aspect of the COVID-19 pandemic has, at one time or another during this pandemic, been hauled up as a reason to deflect from the reality of 2020. The reality is that ineffective, unprepared, slow-to-act and cloth-eared leadership – supported by the cult of wish-it-away – has slowed the response to this pandemic, making things worse. Not just in 2020 but across decades of profit-over-people decision-making.
Leadership needs to lead
Governments that won’t provide universal healthcare can’t look after the mental and physical well-being of their populations, so they haven’t been able to safely take the harsh measures that most effectively break widespread transmission while also maintaining suitable care for the multitude of health needs of those under their care.
Governments that won’t get serious about financial protections for the lives and livelihoods of frontline workers have failed to protect their communities. Instead, they’ve doubled down against the most effective restrictions to prevent bad economic numbers.
Governments that had in place convoluted lab test development regulations and who hadn’t built up testing capacity have instead had to settle for less ideal ways to test people because the gold standard is unachievable. Or it’s just too late.
Governments that failed to invest in and listen to science and public health have not been able to use the power of contact tracing to help contain more transmission and have generally made poor decisions, putting their communities at greater risk.
Governments that have failed to learn from successful countries about subjects like safer return to school, how to reduce restrictions carefully, the importance of multilingual and multilayered communication and education on all facets of the pandemic, and changing the dogma of “droplet” versus “airborne” in response to the screaming pleas of expert aerosol scientists.
There are also the loud angry supporters of those governments who consciously hold fast to and amplify these failings for their own benefit and fame, or because they don’t know any better, or they simply follow other malicious agents of chaos down a dark path of often angry and usually selfish fantasy.
Individual rights over societal good seems to be a doctrine that yields disastrous results for the health of an interconnected world. Who could have guessed this?
But I’ve digressed.
The PCR test works to find infections. It can find them before you become sick, helping to contain the spread if you have a process for isolation.
PCR testing can find an infection if you were sick recently but missed a timely test. Whether you feel sick or not, that means contact tracing can be used to contain transmission chains that you may have started.
PCR can actually be used to slow the spread of SARS-CoV-2 and contribute to bringing an epidemic under control—of course, only if you actually do something to respond to those results.
If you miss transmission chains and cases or find them but don’t do anything to interrupt them, then you simply have to rely on hope and faith that things will work out in the end. So far, hope and faith haven’t helped much.
References
- Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020
https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.32.2001483 - Charting the COVID-19 spread in Australia
https://mobile.abc.net.au/news/2020-03-17/coronavirus-cases-data-reveals-how-covid-19-spreads-in-australia/12060704?nw=0&pfmredir=sm - Statement From The Premier, Victoria, 22NOV2020
https://www.premier.vic.gov.au/statement-premier-82 - Antigen-based testing but not real-time PCR correlates with SARS-CoV-2 virus culture
https://www.medrxiv.org/content/10.1101/2020.10.02.20205708v1 - Singapore’s COVID-19 Interactive Situation Report
https://www.moh.gov.sg/covid-19/situation-report - China COVID-19 cases via the World Health Organization dashboard
https://covid19.who.int/region/wpro/country/cn
Updates
- 28DEC2020: corrected some typos
- 05AUG2024: corrected a few more typos
Great article. I would really like you to comment on these two articles.
Thanks.
https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa1491/5912603
…and…
https://www.thelancet.com/journals/lanres/article/PIIS2213-2600(20)30453-7/fulltext
How are the limit of detection and limit of quantification determined when validating a PCR test method?
Depends on who does it.
Early in the pandemic my lab, as was the case with so many other labs, received our PCR chemistry from a company that had inadvertently contaminated most of the covid N gene test with the template they were producing as a positive control for the test. we ended up with 70,000 reactions worth of this test that had a false positive rate of about 1in 500. However because my lab is competent when we saw a single positive reaction at CT 37+ from a chemistry that we knew was compromised we would rerun that sample three times with that test and three times with a secondary test targeting a different Gene. It sounds excessive but actually the cost of these test is very inexpensive compared to the cost of the manpower required to run them and since we were running several hundred per day rerunning one sample six times did not increase our burden. All of these results were available same day the swab was taken, typically within five or six hours. We found a pretty even mix of those who were shown to be negative and those with late CT values who were positive in all six tests. The ones we were confident were positive were re swabbed the following day and would have CT values in the low twenties. Because we were testing asymptomatic people sometimes we just caught it so early that there wasn’t much virus available to detect and the following day they would be symptomatic with a much higher level of infection.
What a clearly illustrated , well argued piece. Thanks Ian.
I feel like you left out something about false positives: for this type of testing a false positive isn’t harmful. A false negative would allow an infected person to continue to be infecting others. A false positive would mean a person is quarantining when they don’t have to. Just to further point out that false positives aren’t as much of a problem as people seem to think.
There is harm. Lockdowns can result from false positives which weren’t necessary. There is mental harm from them but also from the stress of thinking there are cases in your neighbourhood and that you need to get tested, rush to eth shops to ‘stock up’ and so on.
THANK YOU!
Thanks Ian. It boils down to the use of positive and negative controls in every assay, and the use of sufficient replicates. That way you don’t have to pick some arbitrary Ct cut-off.
Not quite. You accept the Ct based on your expertise in the lab, knowledge of that test, the setting of a useful threshold and your skill in using PCR. And that doesn’t = diagnosis. A PCR result is just one step in the path to diagnosis. A diagnosis is a clinical endpoint, not a lab endpoint.
Ian – Which is why Portugal threw it out as a diagnostic tool absent a patient’s doctor’s input
My understanding of a “false positive” in terms of testing for SARS-CoV-2 is a situation whereby RT-PCR detected the RNA sequence for the virus in the sample, but there isn’t enough virus present for the person to be contagious. Do you concur?
Quote: “In an article published in Clinical Infectious Diseases, Bullard et al reported that patients could not be contagious with Ct >25 as the virus is NOT DETECTED in culture above this value.
This limit was then evoked in the French media during an interview with a member of the French Scientific Council Covid-19 as a possible value above which patients are NO LONGER CONTAGIOUS.
High Ct values are mostly correlated with LOW viral loads.
In rare cases…the PCR is positive beyond 10 days, often at a Ct >30. These rare cases should not impact public health decisions.”
https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa1491/5912603
If one cannot grow virus from a sample with a Ct of 25 – one needs to look carefully at one’s culture protocols, optimisation, training records and validation process.
I feel that this Jaafar et al study is very important to understand, because it has been misinterpreted by a Portuguese court to rule PCR tests unreliable (and hence, quarantines “unlawful”) – and in turn, this ruling has been used by the conspiracy theorists to support their “casedemic” narrative.
Some people are making the ridiculous claim that it shows that at Ct = 35, the accuracy rate is only 3%, with the false positive rate being up to 97%.
What it actually shows (correct me if I’m wrong), is that at this Ct, of the 74 positive samples detected by PCR, only 2 (< 3%) of these were able to infect other cells.
It doesn't help that the language of the French authors seem to obfuscate this reading: "At Ct = 35, the value we used to report a positive result for PCR, <3% of cultures are positive."
The study doesn't mention anything about the reliability of the PCR test.
Well Dr, can you “Riddle Me This?” What about people who get a test sent to them, send it back without even doing the test and get a text from test & trace saying they are positive? It has happened all over the UK….
Perhaps there is some misinterpretation of what people call ‘false positive’. Perhaps they are suggesting that a ‘false positive’ could be a recovered person who is now shedding viral RNA debris, and has been studied this can happen up to 18 weeks after infection, rather than an inherent inaccuracy in the technique. Although you recognise there is that factor, as with anything.
I think the idea that now immune people could then be lumped into the case numbers as positives is what many find objectionable. Especially as it is cases that are still restricting our lives 8 months on. What many call the ‘casedemic’. Many asymptomatic or potentially immune people being logged as cases and being reported with hysteria, but not resulting in hospital admissions or deaths.
So you prove that the RNA can still accurately find it’s target at high CT but also say that this is no indicator of the infectiousness of the Virus and say that the higher the CT to obtain a positive, the less virus there is.
But I also appreciate you describing how imprecise this is and that levels fluctuate throughout the arc of the virus and therefore a high CT cannot say at which stage of the virus the person is, they could be at the beginning or the end theoretically. So it is a complex dilemma that I can appreciate more.
As clearly this kind of disruption cannot be repeated, what would you say is a way to use PCR technique to minimise it? Bearing in mind the IFR’s varying so much between age groups would you choose a protection of the vulnerable approach?
Also what are your thoughts on beta-corona viruses?. There is now mounting thought that this explains T-Cell immunity in people who have had not Sars-Cov 2. Is there any possibility that a beta-coronavirus could create a PCR positive test result?
Sorry for the length, an interesting read that got my brain ticking.
I don’t see that you have proven that false positives dont occur at some level here.
1. You start by describing an example where a control positive clearly stands out from another 72 samples. So no false positives in 72 tests. That might happen randomly if the false positive rate were 1% for example.
2. You explain that 5 of 60 positive tests at 35 amplifications are indeed positive with live virus. So you need that amplification to detect almost all real positives. But by that same statement 55 out of 60 positive tests at 35 amplifications did not contain live culturable virus so were presumably false positives.
3. You discuss the example of Australia and generalise the result to the rest of the world. As Australia has been successful in test and trace containment the virus is not in epidemic or endemic stages there. The prevalance is all but zero and therefore the likelihood of any operational cross-contamination between positive and negative swabs is also very small. But this isnt true of the ROW. In the UK swabs are collected by the person themselves and bagged by them. Someone then grabs the bag with a grabber and chucks it into a cardboard box with 100s of others. All bags contact an infected/non-infected person, the same grabber, and numerous other bags in the same box. Therefore immediate cross contamination possible – especially if there are say 1 or 2% true positives in the population. Testing is also in very high volume – 400,000 a day in rapidly created labs using people with very limited training. Some swab test tubes are found to have leaked from the bag in the box on arrival. These are handled alongside the debagging of the other swab tubes by the same people. Labs are under extreme pressure to process tests quickly in vast numbers. Labs have been allowed to waive quality controls in favour of maximising throughput. No monitoring of operational false positives/negatives appears to take place using known control positives/negatives inserted at the testing stations.
4. Here is the UK statement on false positives for PCR…https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/895843/S0519_Impact_of_false_positives_and_negatives.pdf
No monitoring appears to be in place and the official answer in parliament is that the operational false positive rate for the PCR testing is unknown.
Now tell me that false positives can never be a problem and are always vanishingly small.
1. It might. This is meant to address those who say “any PCR run for more than X cycles” will come up positive.
2. Not false. True positive just not with detectable virus in that sample, using that method at that time. Doesn’t change the fact that those people are all infected.
3. Yes, because Australia is one of a handful of countries not on fire
4. Sorry, but that doesn’t change what this post set out to rebut. False positives don’t just happen with late cycle numbers or even very often at all (<1 in tens or hundreds of thousands of tests when performed by good labs). Yes, when things are completely out of control, this may change, but then so do many aspects of the pandemic under those conditions. Like the percentage of excess deaths.
Your complaints all suggest you didn't read the opening paragraph of the post in which I lay out the scope of what will be addressed.
I’d like to hear your comments on this study: https://www.cebm.net/study/covid-19-testing-and-correlation-with-infectious-virus-cycle-thresholds-and-analytical-sensitivity/
This seems to be specifically looking at culturability of the virus. If it’s not culturable it’s almost certainly not going to be infectious, right? So we see one specimen where a 30 CT cut off would have been a false negative. But with a 40 CT cut off a ton of false positives.
Am I reading this wrong?
What you see really nicely by comparing the single example here and the single example in my blog – is a range of results. As I wrote, stating a single Ct value like 30 or 35 as the cut-off is not even attempting to accommodate that variability. Bad science. People may not be aware that culturing virus is an artform. And it’s even more subject to biological variab ility and the effects of poor specimen transport, collection, storage freezing and so on. The expertise to perform viral isolation by cell culture also sits across a spectrum, just like the expertise of labs conducting PCR.
… culturing virus is an art form. Biological variability, poor specimen transport, collection issues, storage freezing. Viral isolation by culture sits across a spectrum. Lab expertise.
Dammit. I was skeptical before. You’ve explained nicely the 30 or 35 Ct value issue. But my confidence in the test hasn’t improved any. In fact it may have depreciated somewhat.
Being Canadian, how about a hockey analogy? When a player shoots at the net, there’s a lot of finite physic involved. But the player may be tired, or may be getting checked or blocked by the defence or the goalie, there may be a delayed penalty, the puck might hop, or he just might miss. You’ve just defended that the speed of the puck as fairly constant, but that’s about it.
You lost me at “art form”. Isn’t there a Standard Operating Procedure for this test that minimizes all that variability.
There are many protocols and methods for virus culture – but factors beyond the culturist’s control have to be just so, for an isolate to result. Just as there is a lot of spectrum within a phrase like “good at hockey”, there is a massive range in the label, “good at virus culture”. I’ve seen people who just aren’t cut out for the requirements of carefully looking after millions of “children” in a culture flask; something that is essential to successful virus isolation.
Also are you aware of episodes such as the following… https://www.nytimes.com/2007/01/22/health/22whoop.html
Note, I am NOT saying such episodes mean COVID does not exist etc. I am just saying isnt this evidence that problems with false positives CAN occur with PCR testing.
“This particular study found that that from among 5/60 (8.3%) patient samples with a CT greater than 35, infectious virus was still present.”
I’m just trying to understand if this means that only 8.3% of the people that tested positive actually have an infectious level of virus? If so wouldn’t the false positive rate be sky high?
If you’re only worried about missing those five people then I guess you’re not worried about that. But if you’re worried that the other 55/60 false positives will trigger some threshold that closes your kids schools (like here in NYC) then it matters a lot.
The point here is that saying “anything over 30 or 35 cycles is not infection virus – as people do – is wrong. The % isn’t the point.
Good article, but I think a lot of the public will have the same questions as me:
1) You performed this test with the human parainfluenza virus type 4. How do you know the same results will occur with Covid?
2) Is it true, even a tiny fragment of a dead virus will be picked up in this test? In which case, there will be many false positives.
3) Did I imagine it, or did the inventor of the test, Kary Mullis, say it wasn’t to be used for detecting viruses? That was of course, before he mysteriiously died in October 2019, just before the Pandemic.
1) It won’t. But from my epxerience it works the same way with SARS-CoV-2.
2) A certain amount is needed even for this test to produce a signal. Thousands and thousands of negative tests and no positives show that this type of false positive isn’t happening.
3) If he did, he was completely wrong. I tell you this as someone who uses PCR-based tests to detect viruses every week and has done so for over 20 years. You can, of course, believe what you like but I’m not here to lie to you or to sell a book or a vitamin or go on a speaking tour.
“Thousands and thousands of negative tests and no positives show that this type of false positive isn’t happening.”
That’s in Australia right? There are plenty of positives in other countries. How do they make sure they’re detecting current infection and not an already past infection?
As for the economics that sort of response is all fine and well if you’re rich. Much poorer countries whose economy was already on life support have been devastated by the steps taken by their governments.
Why do we do lab tetsing?
So i guess Fauci is wrong again by claiming anybody with a cycle above 35 would almost certainly be inactive virus, can’t be cultured etc?
Yes
Ian, Thank you for your initial response. I wasn’t complaining, I was just pointing out limitations in your argument. You may say your scope is limited to PCR multiplications, but the title of your article is broader and is being cited by some as showing that operational false positives cannot occur in significant numbers. Clearly as you agree this is not correct and there are known cases of PCR testing problems with false positives. Locations under taking large scale testing need to be aware of the danger of PCR operational false positives and apply very tight quality control checks to combat the real risk of pseudo-epidemics.
Take that up with them.
Thank you for the explanation Ian. We have a unique situation where I’m at in the US, our state governor paid a company $120M to build a lab where tests could be evaluated. The state is getting a $5.50 kickback (approx $1M a day). That lab launched Nov 1st, the state is pushing as many tests as possible to go through this particular lab. There is no transparency on the CT’s but our positive cases increased over 25% the day they went on-line. Are labs in Australia transparent where they will post what the CT’s are?
Those data are available to specific people managing the case I believe – but they aren’t posted in the public domain AFAIK
Either you’re an idiot or a liar. After 30 cycles is a USELESS test that’s a fact and covid is a LIE. People like you make me sick.
I love that you are tackling this and engaging with folks. Thank you! My main question I have is I cannot seem to find evidence that a positive result from PCR is equivalent to infectivity. That is an important piece of this issue. When I was developing PCR for wildlife disease we went thru extensive experiments to be able to say our positives are meaningful, in other words demonstrate an infectious individual. I would love to see a study that tries to do this but I can’t find it
Have a look at other recent posts – I have one that shows a linkage between an infectious virus and PCR; multiple times.
Strictly speaking, the question is not about “false positive” but rather about “overdiagnosis” (or wrong diagnosis).
The Australian example is good but we should remeber that the virus didn’t hit them very hard, overall 28k cases out of 25m population, so about 99.9% of the population never had it. Even if we assume the true number of infections was x5 that’s still 99.5%.
There remains the question about other countries where a much larger portion of the population was infected and mostly undiagnosed, for how long unharmful remnants of the viral RNA remain in the blood of a recovered person, weeks? months?
Until we have a good answer to that question, I think that you can’t say for sure that there is no substantial “problem” of PCR “overdiagnosis” of long recovered COVID patients in countries that had significant outbreaks in recent weeks or months. To me it seems plausible, and in agreement with the culture studies, that using PCR test with high Ct value on asymptomatic patients in many cases works similarly to doing a serological test for antibodies, a positive result may mean a past infection and not a current one.
Can this be studied? Of course, by simultaneously doing serological and PCR tests. If the serological test gives IgG positive and IgM negative result it means past infection, and then we can see what percent of those are PCR positive and at which Ct value.
It didn’t hit Australia very hard because we do a lot of testing, we rolled out tests in January, we contact trace well and we locked down our borders as well as any clusters and outbreaks. Not because Australia is different from any other urbanised society. Other countries were slower, never got serious about lockdowns for long enough, had no plan for what to do after lockdowns, gave in to voices calling for returning to profit over society, didn’t support their community through lockdowns, favoured individualism over community…and many other reasons.
Thank you for the very well described workprocess. I came here also because I could not understand why someone would claim more false positives than what I would normally expect to see in a lab. And escpecially claiming that it could have anything to do with number of cycles… That made no sense to me.
I’m guessing a lot of people dont know math 🙂 But I do accept the fact that if prevalence is 0,5%, and testing shows 4% infection rate, then either there are many false positives, or the prevalence is not 0,5% as claimed (statistically that would be my conclusion at least).
I neglected to account for operational reasons for a false positive. Thank you for reminding me…
Hello! I run a science/atheist YouTube channel called Nervardia and I’d love to have you on for an interview.
You’ll be in good company, I’ve had Dr Karl on twice.
It’s best to find me on Twitter @Nervardia
And my channel is http://www.youtube.com/c/Nervardia
Please let me know if you are interested!
Thank you!
Meredith
Sorry but no
Are all of the PCR tests in Australia performed at 40ct? If not, what threshold is standard there?
Depends on the lab and doesn’t define whether a patient is a case without knowing context from other sources as well as what the test Ct result is (which is different from the maximum cycle number you’re referring to)
Hi, I enjoyed reading this article. Would it be okay for you if I translate it to German and publish it in my blog together with a link to the original article?
I’ve given my thoughts on Twitter
Dr fauci and the who have said more than 35 cycles will give false positives and more than 37 is not even worth considering the results.
Link to him saying this please?
Jaffar et al 2021 correspondence further confirms results from 250 566 SARS-CoV-2 RT-PCR (N gene amplification) for 179 151 patients and the results of culture that higher Ct values are mostly correlated with low viral loads (https://academic.oup.com/cid/article/72/11/e921/5912603).
“It can be observed that at Ct = 25, up to 70% of patients remain positive in culture and that at Ct = 30 this value drops to 20%. At Ct = 35, the value we used to report a positive result for PCR, <3% of cultures are positive.”
It’s hard to deny this level correlation by arguing culture technique is highly variable and an art form. We have an example of the same lab performing the same analysis with tons of biological replicates.
In the US breakthrough cases are only sequenced after a positive PCT CT = 28 value and not higher.