I have never used this particular set of primers, but have done a lot of PCR. In general, at 30+ cycles, PCR is prone to spurious amplification. It depends on the primers, temperature profile, and other details, but at these cycle counts you need to be skeptical of your results. It's easy to get noise.
I've never been able to fathom how a PCR amplification at 30+ cycles with no downstream purification or gel visualization is considered definitive diagnosis of an illness. I strongly suspect that the goal was to cast a wide net (i.e. bias toward false positives) at the expense of accuracy, but then "cases" became some kind of top-line media metric...
Then in January the WHO updated the diagnostic protocol [1] because of that false positive/low confidence problem. Unsurprisingly, case counts plummeted in the following weeks.
[1] https://www.who.int/news/item/20-01-2021-who-information-not...
For that reason alone it became another thought-terminating political topic -- you're either dismissed as a conspiracy theorist for correlating these events, or you're dismissing the value of the vaccine rollout/lockdowns/other measures, or you're a sheep following the dominant media narrative.
Reports last year indicated Trump’s own FDA was responsible for setting out the needed time for data gathering and review that pushed it into mid-November. https://abcnews.go.com/Politics/white-house-okays-fda-months...
Meanwhile other countries including China and Russia didn’t approve their own vaccines faster, seeming to indicate the timeline had little to do with U.S. politics.
https://www.nbcnews.com/news/world/putin-claims-first-corona...
https://www.reuters.com/article/us-health-coronavirus-china-...
The first two phases involved just a few dozen volunteers.
Phase 3 trials will be conducted not only in Russia but in partner countries including the United Arab Emirates and Saudi Arabia, Dmitriev said in Tuesday's statement.”
According to https://en.wikipedia.org/wiki/Sputnik_V_COVID-19_vaccine#Aut... the first authorizations outside Russia occurred in December 2020.
Similarly for the Chinese vaccine it took time for the trial results to arrive. Sinovac was approved for general use in February 2021, months after the FDA had authorized Moderna and Pfizer vaccines. https://www.scmp.com/news/china/science/article/3120855/covi...
so what does correlating these events have to do with anything while ignoring verifiable causation, such as the WHO already having documents about these changes going back to September 2020
I don't think you're a kook, and I can only guess what those people were thinking. Maybe they just wondered... and therefore, what?
PCR inventor Kary Mullis is on video calling Fauci out for doing exactly that. Unfortunately I can't even link the two videos because they keep getting memory holed. If you search around you might get lucky, otherwise I'll upload my saved copy when I get off work.
A PI once confided in me that he didn't believe in the big bang. I was startled because creationism was on the rise, and I knew that he was Catholic. However, I also knew he was a natural empiricist, and after taking a quiet moment to think things through, I realized I was being tested to see if I could think critically and ask the right questions as a scientist.
He didn't deny the big bang, and he wasn't replacing it with a worse theory. After a few questions, he demonstrated that his understanding of the evidence and his tools to evaluate it were far better than mine, and that while it was the most probable and best supported explanation, because it was not observed and was not currently reproducible, it wasn't anything that warranted "belief".
Reality doesn't require our consent to exist.
OK? That doesn’t change the massive weight of evidence in favor of HIV causing AIDS.
Moreover, PCR testing during the covid epidemic, which he was not alive for, has clearly been working well. High cases later correspond to high hospitalizations and high covid-19 deaths and high excess deaths across many different countries.
Frankly I don’t put much trust in his Nobel, any more than Michael Levitt who is also a Nobel laureate and has repeatedly made falsified predictions about the Covid-19 pandemic.[2] It seems pretty clear that Nobel prize winners can later lose touch with reality.
In the case of Covid, "hospitalizations" are largely defined as "in the hospital with a positive PCR test", so this is a truism. Deaths are predominantly downstream of "hospitalizations", so again, this is a truism.
Any pathology in PCR testing would equally affect "hospitalizations" and "confirmed deaths".
There is no correlation between COVID health outcomes and levels of testing.
It turned out Mullis had written an introduction to a book called "Inventing the AIDS virus" by a (former?) virologist called Peter Duisberg. This introduction laid out his case quite clearly and the book went into great detail, elaborating a theory about why AIDS and HIV are not in fact linked.
I ended up not developing any strong opinions about the merits of the theory, but I will say that it is a scientific theory and not easily dismissed. To do so would require a lot of detail because the people arguing that HIV isn't the cause of AIDS are scientists and have many scientific arguments.
Here is a brief tl;dr summary of Mullis' argument:
1. In the 1980s when AIDS was newly discovered, he was writing a paper about the use of PCR in the detection of HIV. He wrote "HIV is the cause of AIDS" and decided he should provide a citation for this claim, but he wasn't sure which paper actually established this. To his surprise, when he asked around, nobody else seemed to know which paper he should cite for this either, despite it being a by-then standard belief.
2. As he broadened his enquiries and did more research, he came to realize that nobody knew what paper to cite for this claim because none existed.
3. When he tried to find out why there was no paper proving the link between HIV and AIDS, he concluded the whole thing was built on groupthink and a strong desire by certain researchers for it to be caused by a virus, as the field of virology was at that point in deep distress due to the apparent lack of any serious viruses on the scene after the defeat of polio and the lack of any meaningfully sized link between viruses and cancer.
The Duisberg book then elaborated on exactly what was going wrong in a lot of detail, most of which I've now forgotten. But a few claims really stood out to me and I double checked them after reading the book. My fact checks passed, increasing my confidence in Duisberg's claims:
1. That the gender ratio of AIDS victims is radically different between Africa and the west. In the west, AIDS victims are predominantly men and always have been. In Africa there is no gender skew. This makes no biological sense because HIV is a very small virus and cannot know the gender of its host, let alone know/care whether the host is in Africa or not, at least not according to any current theory of genetics or biology. Duisberg provides a much simpler explanation: once AIDS hysteria reached a high enough point, western aid agencies started handing out money in proportion to reported AIDS incidence in a region, and handing it directly to doctors. Combined with the vague nature of AIDS symptoms (it's a syndrome, so the symptoms are the symptoms of whatever disease your broken immune system can't fight off), this gave a strong incentive for doctors to mis-label cases as AIDS in order to get more cash for their clinics.
I verified this claim against a database held by ourworldindata, if I recall correctly. Although the book is old, the claim is still correct.
2. That at some point people started cropping up who had AIDS but were not HIV+. This posed a major problem to the theory, but it was fixed by inventing a new disease with an incredibly long and technical name that had identical symptoms to AIDS but differed only in not testing HIV+. In other words, at some point having a positive HIV test became a "symptom" of the disease, and cases where it was missing were retroactively redefined as "not AIDS", thus making the theory unfalsifiable.
I verified this claim was true by looking up the Wikipedia page and a scientific paper talking about the "AIDS without HIV" disease and confirming the description. Unfortunately I can't remember now off-hand what it was called. I'd have to dig through the book. I recall Duisberg asserting that the name appeared to have been chosen to be very difficult to remember, and I'm inclined to agree.
Note: the same thing has happened with COVID, in which having COVID requires you to have a positive COVID test rather than any specific symptoms.
3. That (western) AIDS never broke out into the heterosexual population in the way that was predicted. That should have happened if AIDS was in fact caused by a virus and AIDS researchers therefore routinely predicted that it would happen ... but it never did. That makes no sense for a disease caused by a virus.
After reading the book I went looking for debunkings of it. The only ones I could find were very poor and mostly concerned with whether Duisberg should be allowed to speak at all. Of the remainder they made arguments that Duisberg had already successfully tackled in his book, so I wondered if there might have been multiple editions. At any rate, it's clear that "mainstream" AIDS science had chosen to simply ignore the problems flagged by Mullis and Duisberg. Given the behavior of health researchers with COVID science I can easily believe the same problems existed back then too.
If I recall correctly, the gist of his argument is like this:
1. When AIDS was new scientists confidently predicted that everyone who caught HIV would die within a year or so. But then people who were HIV+ kept living longer than a year. Rather than treat this as evidence against the link, 'the science' as we call it these days kept being retroactively changed to stretch the supposed incubation period of HIV. This kept going until HIV was claimed to be able to hide non-active for a decade or more.
2. At some point AZT and other anti-retrovirals were developed. These were extremely toxic treatments because they work by stopping cells dividing. They're more like a form of chemotherapy. The drug trials didn't follow the rules of good trials and became hopelessly corrupted, e.g. patients were able to unblind themselves as to whether they were in the placebo group or not and then started trading with others who weren't. They had been told they were guaranteed to die without treatment, so obviously everyone in the process was highly incentivized to get their hands on this supposed miracle drug via fair means or foul. There were many other problems with the trials but that's the one I remember.
3. Not surprisingly given the nature of AZT, people put on it frequently ended up dead even though they hadn't previously been sick. This was interpreted as a failure of the treatment to treat the finally appearing AIDS, rather than the treatment itself killing the patient. The picture was muddied by admissions that of course this therapy had extreme side effects, but it was justified by the guarantee of death that came with HIV.
4. Nonetheless, they kept decreasing the dosages and mixing it with other drugs to reduce the toxicity of the treatments. This was then written up as improvements in the treatment. Duisberg argues they merely kept making a treatment known to be toxic less so. Because (in his theory) HIV wasn't killing the people in the first place, this then led to improving life outcomes which were interpreted as a success for medicine.
5. At this point the HIV/AIDS theory became unfalsifiable. Because HIV was claimed to be a special virus that might kill you very quickly, or might wait decades to do so, everyone with it was given treatment. If they survived a long time, the treatment was the cause. If they died, HIV was the cause. Regardless of what happened the data was interpreted in such a way as to reinforce the theory. Any evidence that disagreed with it was swept under the carpet or fixed via redefinitions, like the addition of HIV positivity to the required symptoms list for AIDS that I previously mentioned.
If you'd like more background then this article by a former science journalist who worked at the Sunday Times might be interesting. At first he believed what he was being told about AIDS, but eventually decided he was being misled and came to feel guilty about his role in promoting AIDS hysteria. He wrote about his experiences here:
I can't really speak to the arguments you've presented. Frankly, they seem totally explicable for any number of reasons, but it's not my field. My feeling is simply that tons of people who work in the field believe that HIV causes AIDS (it also totally makes sense to me you could have an immune deficiency without some specific virus, but whatever). So I believe it. If tomorrow, it's discovered not to be the case, I'll probably believe that too. It's not my field, so why would I have a strong opinion? What's the point of even reading a book about it, unless you're working in microbiology?
Science is often said to be self correcting. I no longer believe this. Rather it's ridden with groupthink, politics and power games. I watched in 2020 as the scientific "consensus" about COVID models became defined by whichever factions were most aggressive, most shameless and most willing to lie, despite the evidence right in front of my face. Like I said, I never developed a strong opinion on the "HIV not the cause of AIDS" theory, partly because I don't really care. COVID is far more important. But could scientists end up collectively believing something that just isn't true at all for decades? Yeah, absolutely. I totally believe that's not only possible but quite likely. Scientists will still be claiming that COVID models worked well when we're all in care homes.
As to why anyone should care: because how do you know who to listen to, if you don't evaluate their past reliability? You say that you'll believe anything academics tell you because it's "not your field". Sounds like you might be a scientist? I think a lot of us would like to know what's true even in fields that aren't our own, especially because governments have a habit of making the pronouncements of scientists everyone's problem.
I guess part of my feeling is, sure, science has problems (every scientist will tell you that) but are there better institutions to give us actionable information in the middle of a pandemic? My feeling is no. So, even if I accept your diagnosis of science as "groupthink, politics and power games", I'd say that's just humans. All institutions, all fields are like that. Nonetheless, science has a pretty good record for delivering more or less solid consensus assessments, so even if it does need some reform, I think it's a pretty reasonable bet that the consensus is more or less on the money.
On the topic of consensus specifically, I don't believe that's actually true. Science is full of people claiming there's a consensus but often when investigated it turns out not to be true, and instead there is an ongoing attempt to cover up or suppress disagreement. A claim of scientific consensus always needs to be checked, unfortunately, although that check can often be quite an easy one of the form "does someone make some well functioning technology requiring this belief to be correct".
There is no requirement that information come from institutions, let alone that it be actionable. If you look at where the most accurate information has been coming from throughout it's been bloggers, skeptics, bands of anonymous researchers like DRASTIC and so on. It's not good and it's not better than having trusted institutions, but all such institutions have been hopelessly destroyed from within, largely thanks to ideology. I see no reason to continue genuflecting at their feet of their smoking hulks. Perhaps better institutions will arise, or perhaps people will learn how to filter information and make decisions without being told what to do. Or perhaps both.
We're at a point where scientific work is the sum of an enormous number of specialists, most of whom are only marginally able to judge the work of those outside their field.
That implies that, to engage with a scientific fact (say, global warming) you are always engaging with a gigantic aggregate of facts from an enormous variety of disciplines.
It's just not realistic for a layperson to absorb all the literature that leads to a consensus and come to an informed conclusion. Sometimes, people who are experts in their fields can do something on that level, but ultimately, they're making those summary judgements at the mercy of implicit or explicit consensus, hierarchy, reputation - all the elements of group-think that make up institutions.
I think what you're describing in regards to consensus is just what a consensus is. Take evolution for example: you can't imagine a more starker difference in views between like, Dawkins or Lyn Marguiles over what that word means. So there's a 'consensus', in that both of them are evolutionary biologists, but a dissensus insofar as what they mean by that. People, in a vacuum, have an infinite variety of opinions, many of which are superficially similar, but are different on a ton of subtle points.
There are a lot of problems in this kind of setup, but I feel if you're going to call institutions in western society 'smoking hulks' when it comes to trust or credibility, mainstream science is one of the last ones you should come to.
Urban area population density requires different mitigations than rural, except rural communities rely on urban ones as logistics pipelines.
So normalize; mask up, stay home. Prefer all gas, no brakes, based on stats? There may not be enough real people to keep the internet on later.
Nothing about the lockdown was for saving you or me specifically, but systems of behavior we rely on.
https://www.cdc.gov/coronavirus/2019-ncov/hcp/planning-scena...
https://web.archive.org/web/20201216033740/https://www.news-...
[1] https://www.reuters.com/article/uk-factcheck-who-instruction... [2] https://www.reuters.com/article/factcheck-who-pcr-idUSL1N2M1...
Why would WHO feel the need to tell people to read the operating manuals closely? I’m sure its not because the accuracy was too high.
Given that reason, cause and effect would be hard to pick.
That is certainly more likely and believable than some vast left-wing conspiracy to implant Bill Gate's microchips in to your iPhone carrying ass to "track" you.
:)
Things like that make people suspicious, and make it easy for people who don't know the difference between a quantum dot[1] and a microchip to misunderstand when Bill Gates calls for a national tracking system[2].
1: (a quantum dot to store medical information beneath the skin really was funded by Bill Gates)
https://news.mit.edu/2019/storing-vaccine-history-skin-1218
2: https://www.forbes.com/sites/mattperez/2020/03/18/bill-gates...
To take control of the government or for good PR/propaganda? Governments have never had any issues conspiring and lying to the public, remember when Fauci said not to use masks because they didn't help? Or those WMDs that we will surely find any day now?
Look, I am not defending anyone, I am saying that _all_ things of this nature are political.
PCR determines how many exponential amplifications are necessary to get a detectable amount of the target RNA sequences.
The amount of that target RNA floating around in the environment does slightly impact the base amount present in even covid-negative patients.
The most sensitive tests have a limit of detection of a couple hundred copies/ml, and the collection kits usually use 1ml of VTM or equivalent. I find it hard to believe that a significant number of people will have enough viral RNA in their nose to put hundreds of copies onto a swab unless it's their own body that's producing those copies.
This has been confirmed in studies. Researchers have taken samples that are PCR positive at various cycle counts, and tried to culture viruses from them. Here's one:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7427302/
"RT-PCR cycle threshold (Ct) values correlate strongly with cultivable virus. Probability of culturing virus declines to 8% in samples with Ct > 35 and to 6% 10 days after onset; it is similar in asymptomatic and symptomatic persons."
(Note: this is not the only one of these papers that has been published. This is just the first one I found with a quick search.)
Its quite possible, especially if there is a testing bias toward people who are less likely to have the disease
All the data we have indicates that false positives on PCR are extremely rare. The only place it gets fuzzy is the definition of positive. People who were previously infected can test positive, and people with very mild infections can also test positive. People who have never been infected though essentially do not test positive.
At 30+ cycles, you are generated false positives off of both everyday Common Cold coronavirus, influenza and probably even bacteria. Literally you are amplifying noise and then calling it a positive.
Factories and meat packing plants used negative PCR tests to create their own bubbles and keep them running.
There is large positive economic value to a highly sensitive test with a small false negative and a larger false positive. There is much less economic value in a test that allows escapes (rapid tests).
A hammer is a great tool. It is not a great tool for repairing broken pottery.
PCR is the ideal tool if you want to detect infinitesimal amounts of a specific nucleic acid sequence. It is not a great tool if you want to use it to define "illness" or "infectivity", for it cannot tell you anything about those questions.
Can you use PCR to cast the widest possible net, and isolate literally everyone who has any shred of viral RNA? Yes. That's essentially what we've been doing. It is a strategy, and this strategy is appropriate in some situations. This strategy becomes a problem when you forget that you're allowing a lot of false positives to be caught up in the process, and start behaving as if "a positive" is a meaningful clinical diagnosis. Now that we have highly effective vaccines and are out of the acute phase of the crisis, it's time to adjust our definition of "infection" to more accurately reflect the true clinical meaning of the word.
Should cases not be an important metric for people to know?
As vaccination efforts have rolled out, there is still a relationship between positive cases and deaths, however the ratio of cases to deaths has dropped dramatically.
If you Google "uk covid cases" and flip between new cases and deaths you will notice that the "2nd wave" in December/January had an increase in deaths 2 weeks after the increase in cases. The "3rd wave" has had a large increase in cases but no resulting massive increase in deaths.
The only metric the public should be concerned about is whether they have or have not been vaccinated.
That would be quite stupid. Because if the risk of the disease is low, vaccines does not make sense when you do risk/benefit calculation.
Hence the people should know about the cases.
Of course, instead, if you are looking to push vaccines no matter what, you would say something like
>The only metric the public should be concerned about is whether they have or have not been vaccinated.
The risk of symptomatic illness is low if you are vaccinated. The risk of symptomatic illness is high if you are unvaccinated. The risk of death is high if you are unvaccinated and have pre-existing conditions and are under the age of 65. The risk of death is very high if you are unvaccinated and over the age of 65.
If the no of cases is nearly zero, that means the virus is no longer dangerous, so it does not really matter at that point.
Not a shocker that the media would sensationalize things.
Science and PCR amplification... has a much looser definition with the possibility for much more false positives with such small number of cycles of amplification.
It was done ostensibly for cautionary purposes but the media seized on it and painted red death map visualizations for people to see with inflated death counts.
There is no indication of inflated death counts. Death counts from covid correlate closely with excess deaths.
Some have claimed that deaths did rise but because of lockdowns, however in “locked down” regions where reported Covid cases and deaths were low, so were excess deaths.
Cause of illness is linked to cause of death and they will track proportionally.
When 100,000 people are reported to die of covid in the USA or another western country with a high quality reporting system, in the same region and time around 100,000 more deaths from any cause are recorded than would normally be expected. Therefore, there’s no reason to believe the covid-19 deaths are inflated (the “with covid not from covid” theory).
Edit: see for instance https://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/t... which is visually quite striking. Figure found in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7852240/
https://ourworldindata.org/excess-mortality-covid
"The raw death count helps give us a sense of scale: for example, the US suffered roughly 360,000 more deaths than the five-year average between 26 January and 3 October 2020, compared to 209,000 confirmed COVID-19 deaths during that period."
The Covid death counts may be correct or a even little lower than expected then.
Further confirms my thoughts that I would not like to be an 80 year old with two co-morbidities around Covid.
Try some math: 360,000 deaths higher than average over 251 days is 1434 excess deaths per day. From Oct 4 through yesterday is another 296 days, and 1434x296=424,464, so we're talking about a scale of around 780,000, which very much supports the total US COVID death count of 627,370.
If you think that's all 80-year-olds with multiple pre-existing conditions, and that you therefore have nothing to worry about, then I hope for your sake and the sake of those around you that you aren't proven wrong by an ICU stay.
Read my comment again.
That's a feature not a bug.
Whose to blame for Lobotomies winning the Nobel Prize?
Whose to blame for Thalidomide being widely distributed?
Almost anything can be passed off as legitimate without accountability with a concerted effort by 'authorities' and the 'news media', it's even worse in the modern short attention span news cycle.
Starvation is natural. Death by predator is natural. Death due to exposure is natural. Death due to disease is natural. Tornadoes are natural. A biosphere-disrupting asteroid impact is natural. There are other things that are natural that are positives too, but it's good, I think, to keep in mind that "natural" doesn't always imply "good."
It could be that a bit more than 625,000 people have died in the US due to COVID. Or it could be higher than that, and it may be a couple of years before we know for sure. It's not lower, though. Not at all.
“Most tests, like the Broad Institute test used by MIT, use a 40-cycle protocol. If the virus isn’t detected within 40 amplification cycles, the test result is negative. If viral RNA is detected in 40 cycles or less, the PCR machine stops running, and the test is positive. Because you received a positive result, we know that the test detected the virus in your sample by the time it reached its 40-cycle limit.”
https://medical.mit.edu/covid-19-updates/2020/11/pcr-test-re...
[1] https://www.politifact.com/factchecks/2021/jun/03/tweets/cdc...
https://www.aacc.org/science-and-research/covid-19-resources...
I'm not sure I even understand the statement, but I guess it means it could be that they (somehow) couldn't report them even if they wanted to.
[1] https://medical.mit.edu/covid-19-updates/2020/11/pcr-test-re...
So, yeah, rest assured, labs work really hard to make sure they report honestly and accurately. Better to fail an occasional proficiency test and repeat, than get sideways on the inspection.
My question refers to blinded testing meaning the lab in question does not know which, and handles, [in this case unexposed swabs from the factory] and it might range around 1-2% of samples on a continuing basis. To me that is the more industrial and continuous connotation of "QC". And the potential importance of "blind" testing.
AFAIK, in any hospital lab there are tests which are still sent out, because they are either more challenging to build and train the right [accurate, low-error] procedures around, or too rarely done for the local investment. What if PCR tests for Covid were also too challenging to ramp up to mass scale in a regional startup lab? There are reports around of horrible controls -- perhaps true or not. That is something sending "blinded" samples through, proportional to mass testing being done, could disclose.
Again, in the industrial setting there is the procedure you reported to the last ISO9000 auditor, and there is the actual procedure. The true spirit of that is that you should also build in procedures to detect when the production procedures are not being followed. Again back to ongoing QC.
I suspect we are framing in terms of two different, almost non-intersecting kinds of institution.
My impression is of reports of "startup" regional labs which have scaled immediately in a pandemic, reportedly hired off the street (not people whose specific vocation and training and life-choice is toward lab technician or manager or scientist), and have resulted in anecdotal reports -- all heresay technically -- of swabs being left lying about in quantity, picked up off the floor, etc etc etc. To me these reports -- perhaps false -- do not intersect with the concern with detail in a lab that knows how to prevent cross-contamination when running at very high PCR amplifications.
I am not bringing any new evidence to this, so I will leave it with clarifying the focus of my concern. I appreciate your standing up for the integrity and integrity-of-process in established labs.
--
s/the lab in question/the startup lab in question/ a level or two up
Note that the US CDC is using two different CT values: a higher one for unvaccinated and a lower one for vaccinated. That doesn't make any sense until you start thinking Hobbsian/Hegalian/Machiavellian.
If I was wanting to exploit the situation, this is exactly what I'd do. Instead I have ethics however.
To me this seems like a much more plausible explanation for dual thresholds than some kind of conspiracy to inflate numbers for political reasons. Immunology is not my field though.
That's my translation of the document I found when looking into this issue. More details below...
===
"CDC is suggesting CT value of 28 for detecting breakthrough infections after vaccinations... So that means, a breakthrough infection needs to have 128 times viral load in someone who has been vaccinated to be considered as positive, than it is required to have considered as positive in a non-vaccinated person."
This sounded strange to me, so I searched for more information about it. It looks like you just misunderstood the CDC's policy.
This document regarding breakthrough case investigations was the second result in a Google search for "cdc ct value 28". The relevant text can be found on page 5 of that document.
https://stacks.cdc.gov/view/cdc/105217/cdc_105217_DS1.pdf
"If SARS-CoV-2 sequencing will not be performed locally and a specimen is available, the state public health laboratory should request the residual clinical respiratory specimen for subsequent shipping to CDC. For cases with a known RT-PCR cycle threshold (Ct) value, submit only specimens with Ct value <=28 to CDC for sequencing."
In other words... Imagine some lab just found a breakthrough case. And this breakthrough case had an especially high viral load (Ct 28). And the lab was just going to report a positive and throw away the sample...
Imagine the CDC yelling: "Don't throw that away! I need more details! Please! If you won't finish the job, please let me do that work!"
That's what the document is saying. There's a rare event that needs extra analysis. CDC is just letting the labs know in advance that if they ever see this event, and didn't have the resources to fully analyze it, please send that sample to the CDC so it gets the attention it deserves.
Nothing to do with whether the test is considered positive or a breakthrough - just about whether to put extra effort into gathering more details on that particular case. CDC is volunteering to do this extra effort only for higher Ct values. Whether or not they do this extra work, it's still a positive result either way.
anyway here is what I have responded to a similar comment
No, CDC isn’t messing with the tests like this. And all this fancy talk about CT values is just cover for a false statement about CDC policy.
This is the actual document that provides guidelines to labs to assess breakthrough infections
https://www.cdc.gov/vaccines/covid-19/downloads/Information-...
but it is no longer available at that location, for some reason, and here is a link to the old version..
https://web.archive.org/web/20210429184157/https://www.cdc.g...
Also, nice try to look up and discredit what I am saying on the basis of the age of my account. I am afraid such tactics won't fly well here.
Covid has both pre-sympomatic AND asymptomatic transmission. This has been proven.
In many places, a negative PCR test means you do not have/carry the disease and can participate in risky activities. The NFL, and the NBA, did this. Movie studios did this. Australia and New Zealand did it as a whole country.
To do that, you need a very sensitive test, not something that only confirms symptomatic infection.
Of course, a very sensitive test has more false positives. But you have to weigh that with the possibility of an outbreak among those who tested negative. Imagine what would have happened if NBA had an outbreak after PCR tests--"The Tests Are USELESS!" the media would say.
How many false positives? Look at how many players sat out during the NBA bubble.
Now back to breakthrough infections. The CDC's thought is that vaccines protect well against existing strains, and their guidelines follow that assumption. Nothing in their guidelines accounted for the Delta, though they are changing their stance now, but slowly.
Now, that makes sense.
But you have also take into account that these are not just numbers. But these are numbers that can destroy countries and communities by implying perpetual lockdowns.
It becomes even more comical that RT-PCR does even when positive, does not imply presence of the virus, but some fragments of a dead virus or even genetic material of some other viruses.
I can only be appalled at the indifference of these people to mandate lockdowns that destroy lives and businesses, based on positivity rate of such a test.
In his German language podcast Dr. Drosten, a Coronavirus specialist from Charite Berlin, is addressing this exact issue. In case you have never heard of him, his lab was the first to publish a working PCR test protocol for SARS-CoV-2 back in January 2020 [1]
Here is an DeepL translated excerpt from the transcript for his latest podcast [2]
"The whole thing has a certain complication. The Ct values that we have here are not easily comparable between the individual test manufacturers. Basically, you can say that a high Ct value always indicates a low viral load. And if the Ct value then becomes lower, then that also becomes a higher viral load. But we can only compare them numerically as long as we are in the same test system. The differences there are sometimes considerable. There are test manufacturers where a value of, let's say, 25 is nothing at all worrying, while the same value of 25 in another manufacturer's test shows that this is already a seriously infectious concentration. This is simply because these test manufacturers do not standardize on the Ct value. That would not make sense either. Instead, it makes sense to simply determine what lies behind the Ct values, namely the actual viral load. You can do that, you have to calibrate that."
and further
"We did that in the fall. All the laboratory work that is necessary for this was done in September and October. I had already explained that to the public in the summer, how that works. We worked in the lab to make this possible. We have also come so far that viral load standards... You really have to imagine it as a small plastic vial with a test solution in it. It contains killed virus of a known, defined concentration. You can order it in two or three defined concentrations from a company that sells such a thing. The purpose of this company is to provide quality assurance for laboratories and to offer the necessary calibration standards. And these calibration standards are produced here in our laboratory, this killed and exactly quantified virus. So we have produced this calibration standard. We have also developed instructions, which are then recommended by the Robert Koch Institute, on how the laboratories can use this calibration standard to convert their Ct values into viral load ranges, which either actually lead to an exact viral load or which - and this is our recommendation - lead to assessment ranges. And that is to an assessment of highly infectious, low infectious, and borderline. So roughly speaking, that is expressed a little bit more genteel and precise. There's even a recommendation on how to express that on the medical findings then. Medical laboratories can do all that. This is also done in practice in the hospital sector. routinely used for discharge decisions. For example, a patient is in the intensive care unit. He is getting better. He should be transferred to a normal ward. Now the question is: Can we do that? Is he still highly infectious? Then a quantitative PCR test is carried out with these findings."
[1] https://www.eurosurveillance.org/content/10.2807/1560-7917.E... [2] https://www.ndr.de/nachrichten/info/coronaskript306.pdf
I have looked and I cannot even find how increasing CT values affect the false positive rate for the PCR testing. If my understanding is correct a single increment of CT essentially doubles the sensitivity of the test, so difference between CT value of 35 and 40 is 32 fold.
CDC is suggesting CT value of 28 for detecting breakthrough infections after vaccinations. And if I am not mistaken, a lot of places was using 35 for the CT value in RT-PCT tests.
So that means, a breakthrough infection needs to have 128 times viral load in someone who has been vaccinated to be considered as positive, than it is required to have considered as positive in a non-vaccinated person.
That is quite ridiculous.