COVID-19: is the Cycle Cutoff Value (Ct value) for PCR Tests Way Too High? Thus False Positives Used to Justify Tyranny and Destroy Lives
Real science is never settled, and anyone who has certainty on such things is not qualified to discuss it — Lloyd Chambers. That applies to climate science, COVID-19, and Einstein’s theory of relativity.
Are we destroying lives and accepting government tyranny based on junk science? Maybe “soaring coronavirus infection rates” are little more than bad science and government propaganda?
Maybe not, but how do we know that, given arbitrary interpreted tests being used.
Infections do seem to be rising (seemingly hard to dispute), but could they be substantially less than claimed, bad bad science (false positive PCR tests)?
NYT: Your Coronavirus Test is Positive. Maybe It Shouldn’t Be
What Happened to Dr. Fauci's Earlier Concerns About COVID Test Sensitivity?
Experts: US COVID-19 positivity rate high due to 'too sensitive' tests
Cycle Cutoff Value
The Ct cutoff value for COVID-19 testing determines whether a positive result is obtained. But the Ct value does not appear to have been chosen in a scientifically rigorous way.
If you know math, consider the potential error with even a small change in input when amplifying by 2^40 times (1,099,511,627,776) times. “PCR commonly uses 40 cycles of amplification, and each cycle doubles the target DNA”.
In particular, the Ct value is set quite low, and thus could be generating large numbers of false positives. And is the test even targeted specifically enough to avoid results from other similar viruses.
Thus we have a situation in which the COVID-19 tests might be mostly phony baloney versus the true infection rate—false positives leading to poor decisions at every level.
The WHO equivocates on the Ct cutoff value. Shouldn’t we know with certainty what is scientifically valid, and what is not? Why is an “update” needed?
Up to 90 percent of people tested for COVID-19 in Massachusetts, New York and Nevada in July carried barely any traces of the virus and it could be because today's tests are 'too sensitive', experts say.
The Ct cutoff value is ARBITRARY, it is “interpreted” and “qualititive”. Sounds like JUNK science. Where are the references to gold-standard scientific studies on the PCR test, that prove-out what is fact vs fiction with respect to infections?
Can a Ct value determine how much viral genetic material is present in an individual patient specimen?
A Ct value does not indicate how much virus is present, but only whether or not viral genetic material was detected at a defined threshold. RT-PCR tests can be either qualitative or quantitative, and this affects how a Ct value is interpreted. As of October 23, 2020, all diagnostic RT-PCR tests that had received a U.S. Food and Drug Administration (FDA) Emergency Use Authorization (EUA) for SARS-CoV-2 testing were qualitative tests.
- In a qualitative RT-PCR test, known amounts of virus are used during the development of the test to determine what Ct values are associated with positive and negative specimens. A Ct value is generated when testing a patient specimen. The Ct value is interpreted as positive or negative but cannot be used to determine how much virus is present in an individual patient specimen.
- In a quantitative RT-PCR test, a range of known numbers of genome copies, called reference samples, are tested alongside each RT-PCR reaction. By comparing the Ct value of a patient specimen to the Ct values from the reference samples, the test can calculate the copy number of target nucleic acid. The correlation between Ct value and viral load can be used in evaluating data from groups of people in categories such as symptomatic or asymptomatic and can be applied to infer the difference in the relative amount of viral load between the two. Although a quantitative RT-PCR test can estimate the level of viral load in a population, a quantitative RT-PCR test cannot determine how much virus is present in an individual patient specimen.
If a Ct value can be affected by factors like specimen collection, how do I know if my RT-PCR test result is accurate?
In addition to detecting SARS-CoV-2 genetic material, each RT-PCR diagnostic test also detects a small portion of a patient’s genome. Detecting the patient’s genetic material in the specimen confirms the quality of the specimen and the processing steps of the test. If the patient’s genetic material is detected, then we can be reasonably sure that the viral genetic material was not degraded, and the test result is accurate.
Can a Ct value predict how infectious an individual with COVID-19 is?
For both qualitative and quantitative RT-PCR assays, the correlation between Ct values and the amount of virus in the original specimen is imperfect. It is therefore problematic to infer any relationship between an individual patient’s Ct value and their viral load. Ct values can also be affected by factors other than viral load. For example, if the specimen is not collected or stored properly or the specimen is collected early during the infection, the Ct value may be higher than it would be under ideal conditions. Thus, a high Ct value could also result from factors not related to the amount of virus in the specimen. The correlation between Ct and viral load can be used to evaluate data from groups of people and infer the difference in the relative amount of viral load between the two groups (e.g., between symptomatic and asymptomatic individuals).
Can Ct values from different RT-PCR tests be compared?
No. For a given RT-PCR diagnostic test, the genetic material from a patient sample must be processed using a specific series of steps to produce a valid test result. However, the steps used to process the genetic material, the specific genetic target being measured, and the amount of the patient sample used varies among RT-PCR tests. Because the nucleic acid target (the pathogen of interest), platform and format differ, Ct values from different RT-PCR tests cannot be compared.
YALE: Your Coronavirus Test is Positive. Maybe It Shouldn’t Be. Published in New York Times, August 29, 2020 Discussion from a hospital laboratory perspective by Marie L. Landry, M.D. Director, Clinical Virology Laboratory, Yale New Haven Hospital
This article is misleading in that it also does not address the validity of the test values in uninfected patients, instead arguing for low thresholds essentially “just in case”. Credibility is thus low.
Conclusion: Response to NY Times article from the perspective of a hospital COVID testing laboratory
- Highly sensitive tests are essential for acutely ill hospitalized patients as virus titers in the upper airway may be low (Ct >30 or Ct >35). However, recovering patients, now non-infectious, may also have a very low positive PCR result.
- For diagnostic testing in the community, delays in obtaining testing, as well as sample type and quality, can lead to higher Ct values at diagnosis. Not reporting positive results with Ct >30 would be a disservice to these patients.
[What about large numbers of false positives from too-low a Ct value?]
- Reporting Ct values alone can be misleading, especially since Ct values can vary significantly between various tests and labs. However, a result comment for low positive results may be helpful. Ct values >40 may be of questionable value.
- It is essential to confirm actual test sensitivity, determine the goals of testing and understand the tradeoffs in various groups: e.g. asymptomatic screening, symptomatic patients, pre procedure, L&D, high risk nursing home residents. •
[YES, because lives are being destroyed by government policies relying on tests that may be dubious at best because of false positives]
- Tests with rapid but somewhat less sensitive results may be acceptable in some outpatient settings, especially when frequent repeat testing is performed.
This article is very weak in that it does not address the false positive issue but instead tries to persuade as to the value of the test while refuting other claims in the news. It lacks credibility as to objectivity because no effort is made to address the false positive issue e.g., the Ct value and its import.
The guideline states:
- There are no reliable studies to definitively prove a direct correlation between disease severity / infectiousness and Ct values. Viral load does not have much role in patient management.
- Ct values differ from one kit to the other. Comparability of Ct values among different kits is a challenge as our labs are using a mixed basket of kits now with different Ct cut-offs and different gene targets.
- Ct values also depend on how the sample has been collected. A poorly collected sample may reflect inappropriate Ct values. Besides, Ct values are also determined by technical competence of the person performing the test, calibration of equipment and pipettes and analytical skills of the interpreters.
- Ct values between nasal and oropharyngeal specimens collected from the same individual may differ. - Similarly, temperature of transportation as well as time taken from collection to receipt in the lab can also adversely impact Ct values.
- Samples from asymptomatic/mild cases show Ct values similar to those who develop severe disease.
- Patients in early symptomatic stage may show a high Ct value which may subsequently change. In such cases, high Ct values will give a false sense of security.
- Severity of COVID-19 disease largely depends on host factors besides the viral load. Some patients with low viral load may land up in very severe disease due to triggering of the immunological responses. Hence, again high Ct value may give a false sense of security.
- Moreover, the RT-PCR test presently being conducted is qualitative in nature. Ct values may give a rough estimate of viral load. However, more specialized standards are required for quantitative assays which are currently unavailable for SARS-CoV-2.