In a widely circulated video, Kary Mullis stated:
"If you could say... if they could find this virus in you at all, and with PCR, if you do it well, you can find almost anything in anybody. It starts making you believe in the sort of buddhist notion that everything is contained in everything else. Because if you can amplify one single molecule up to something that you can really measure, which PCR can do, then there's just very few molecules that you don't have at least one single one of in your body. So that can be thought of as a misuse of us, just to claim that it's meaningful."
The quote comes from a July 1997 meeting and the context was related to Mullis's denial of the well established fact that HIV causes AIDS.
There are only 4 distinct DNA molecules. SARS-CoV-2 PCR tests look for a fragment consisting of numerous molecules in a sequence that is unique to SARS-CoV-2. This pattern is validated to ensure it does not exist in the human genome or other known pathogens.
The amplification process (repeating cycles) improves the chance of detecting a match that IS ACTUALLY PRESENT. Additional cycles do not lead to finding things that aren't actually there.
This CDC webpage is often referenced for this claim: https://www.cdc.gov/csels/dls/locs/2021/07-21-2021-lab-alert-changes_CDC_RT-PCR_SARS-CoV-2_Testing_1.html
After December 31, 2021, CDC will withdraw the request to the U.S. Food and Drug Administration (FDA) for Emergency Use Authorization (EUA) of the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel... CDC recommends clinical laboratories and testing sites that have been using the CDC 2019-nCoV RT-PCR assay select and begin their transition to another FDA-authorized COVID-19 test. CDC encourages laboratories to consider adoption of a multiplexed method that can facilitate detection and differentiation of SARS-CoV-2 and influenza viruses.
Many have misread this language to suggest that the CDC test detects both SARS-CoV-2 and influenza, and is unable to distinguish them, therefore influenza is recorded as a positive result for SARS-CoV-2. THIS IS FALSE. The CDC test could only detect SARS-CoV-2, therefore there was no need for it to differentiate SARS-CoV-2 and influenza viruses.
Since the CDC test was originally developed, the commercial labs have developed tests that can detect AND differentiate both SARS-CoV-2 and influenza. In other words, the new tests can do 2 tests in one.
The CDC clarified the bulletin saying "CDC is retiring the CDC 2019 Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel because the U.S. Food and Drug Administration (FDA) has authorized hundreds of other SARS-CoV-2 diagnostic tests, many of which are now higher throughput or can test for more than one illness at a time."
The CDC test is to be discontinued at the end of 2021 because newer tests save time and resources by incorporating 2 tests (SARS-CoV-2 and influenza) into one process, NOT because it had any problems detecting SARS-CoV-2 reliably.
There is no particular optimal cycle count. The laboratory that develops the test validates their own process and determines the cycle count that is appropriate for their application.
High cycle count does not drive false positives, but may be more likely to detect remnants of dead virus that haven't yet been completely destroyed.
The cycle threshhold or Ct value indicates on which cycle a match was detected. A test set to run for 40 cycles might have a Ct of 30, for example. The additional cycles are irrelevant at that point (except in practice, many individual samples are tested at the same time, and each might have a different Ct value, so the test continues until it reaches the configured cycle count).
The Ct value can give a general idea about how much virus was found. For example, a Ct value of 20 would indicate far more viral material in the sampel compared to a Ct value of 40.
This section needs references.
RT-PCR or Reverse Transcription PCR is used to detect RNA viruses such as SARS-CoV-2
Real Time PCR (not to be confused with RT-PCR) means that the machine checks for a match after each cycle and records the Ct value (the cycle on which the match was detected).
RT-PCR could be run in real time or conventionally, but in practice, all Covid tests would be run with real time RT-PCR.
Cycle count - the number of cycles that the machine runs
Cycle threshold or Ct - the number of cycles that ran before a positive result was returned.