CDC Specifies PCR Test Cycle Threshold For Vaccinated Individuals: What Does This Mean?

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by Arjun Walia, Collective Evolution:

  • The CDC is and will be collecting samples from COVID tests of vaccinated individuals to try and determine if the virus can breakthrough the protection of the vaccine. In doing so the CDC has specified a cycle threshold for PCR tests.
  • Reflect On:Why a cycle threshold suddenly? Why not one prior to the rollout of vaccines? How many false positives have we seen as a result of no prior cycle threshold? Will PCR tests of the unvaccinated have this new cycle threshold?

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The CDC is monitoring COVID-19 “vaccine breakthrough” cases at the moment. This means that those who are fully vaccinated with the COVID-19 vaccine can still become infected. According to the CDC, “a small percentage of people who are fully vaccinated against COVID-19 will get sick and some may be hospitalized or die from COVID-19.”

Throughout this pandemic, the tests used to identify “positive” COVID-19 cases has been the reverse transcriptase-polymerase chain reaction (RT-PCR) test, which can detect the virus in nasal swabs (RT-PCR). The PCR test is not actually designed to identify active infectious disease, instead, it identifies genetic material, be it partial, alive, or even dead.  PCR amplifies this material in samples to find traces of COVID-19.

The CDC is requiring that clinical specimens for sequencing should have an RT-PCR Ct value ≤28 when conducting tests for vaccinated individuals. “Ct” refers to cycle threshold.

According to Public Health Ontario,

The cycle threshold (Ct) value is the actual number of cycles it takes for the PCR test to detect the virus. It indicates an estimate of how much virus was likely in the sample to start with – not the actual amount. If the virus is found in a low number of cycles (Ct value under 30), it means that the virus was easier to find in sample and that the sample started out with a large amount of the virus. Think about it like the zoom button on your computer, if you only have to zoom in a little (zoom at 110%), it means that item was big to start with. If you have to zoom a lot (zoom at 180%), it means that the item was small to start with.

Why This Is Important: It’s been difficult to find what PCR Ct value tests have been using during this pandemic, and it’s important because at a value at 35 or more for example, an individual is more likely to test “positive” when they are not infected and/or do not even have the ability to transmit. This is commonly known as a “false positive.”

There are multiple studies showing that the number of “cycles” performed by PCR to amplify the genetic sample is directly correlated with infectiousness. The more cycles needed to get positivity from a sample, the less viral replication, or “positivity” for lack of a better word, the sample shows.

For example, an article published in the journal Clinical Infectious Diseases found that among positive PCR samples with a cycle count over 35, only 3 percent of the samples showed viral replication. The cycle number is associated with the chances of infectiousness, yet this has never really been available to the patient nor the public. Most people don’t even know about it. The study examined 3790 positive samples with known CT values to see whether they harbored viable virus, indicating the patients were likely infectious. La Scola and his colleagues found that 70% of samples with CT values of 25 or below could be cultured, compared with less than 3% of the cases with CT values above 35. Cultured basically refers to the ability of the sample to find the virus and determine an infection.

This could be interpreted as,

“if someone is tested by PCR as positive when a threshold of 35 cycles or higher is used (as is the case in most laboratories in Europe & the US), the probability that said person is actually infected is less than 3%, the probability that said result is a false positive is 97%.” (source)

According to Stanford Medical Professor Dr. Jay Bhattacharya, PCR samples with a cycle count over 35 is a common lab occurrence. This means that if during this pandemic this was the case, the number of false positives could have been over 90 percent, meaning the vast majority of positive cases weren’t really positive. It means the number of positive “cases” were not an accurate picture of how many people were actually infectious and capable of transmitting the virus. This was and still remains a concern, because “cases” all over the world are being used to set health policy.

Bhattacharya explains in his article,

Dr. Anthony Fauci himself told This Week in Virology in July, “If you get a cycle threshold of 35 or more … the chances of it being replication-competent are minuscule.” Why then has our national testing standard never reflected this? PCR providers should work with other labs to perform a random viral culture on those who received positive results, to validate their tests in terms of being an indicator of infectiousness. Other states should emulate Florida in requiring laboratories to report cycle times to providers and to public health officials so they can provide better advice to patients and make more nuanced decisions about mandatory quarantine orders.

The World Health Organization (WHO) didn’t properly address this issue, it seems, until nearly a year into the pandemic, when they put a notice on their website. They did however already make it clear that WHO guidance Diagnostic testing for SARS-CoV-2 states that careful interpretation of weak positive results is needed (1). The cycle threshold (Ct) needed to detect virus is inversely proportional to the patient’s viral load. That being said, I still couldn’t find what cycle threshold was being used in any part of the world, you would think this type of information wouldn’t be so hard to find?

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