Questions Not Asked: NSW Still Using RT-PCR Cycle Thresholds of 40-45

There may be good reasons for NSW Health to specify RT-PCR cycle thresholds (CT) of 40-45 for Covid-19 testing. Even despite evidence since mid 2020 that thresholds above 25-35 can create false positives for disease and infectivity. But we don’t know if those reasons even exist, or what they are if they do.

We don’t know because our media are too dumb to ask questions, and our bureaucrats are spin-doctoring drones who obscure all relevant data.

You can find a simple explanation of RT-PCR cycle thresholds here. You’ll need it to understand what follows. The basic idea is that the threshold represents how many times you have to use RT-PCR techniques to double the viral fragment you’ve found before it becomes detectable. Each number represents a doubling, so the difference between 35 cycles and 45 cycles is 2^10, or 1024 times larger.

As the WHO states, “the cycle threshold (CT) needed to detect virus is inversely proportional to the patient’s viral load.” That is, the more cycles you need to get a positive, the less virus is present.

The Issue

There is substantial evidence that when PCR cycle thresholds are too high (too much replication before detection), they can indicate someone is a Covid case with active disease, or could be infectious, when they aren’t. This is the idea of false positive. Tony Fauci highlighted the meaninglessness of cycles >35 in July 2020 – for what his word is worth (quote).

This type of false positive comes about when there are some RNA elements of SARS-Cov-2 virus present, but it’s not enough to make you sick or infectious. It could even be a leftover from being sick up to 2 or 3 months prior.

This does not include wrongly capturing other coronaviruses, or showing positive when there is no virus present at all. Those are different questions that include issues like contamination, non-specific genetic targets and similar. These also lead to overstating Covid case numbers, but are not what I’m talking about (list).

What is too high? The best guesses from current research (shown below) are that:

  • Probably not sick, almost certainly not infectious: if a person is only found positive above 35 cycles then they are unlikely to make themselves or anyone else sick. (see References)
  • Maybe sick, probably not infectious: it is unlikely anyone is infectious if only found positive above 25 cycles, but they may have active disease (see References).

To remind you: NSW has always set the cycle thresholds at 40-45. Even the New York Times realised this problem…in August 2020.

This means that during mass RT-PCR testing many people with no symptoms and who are not infectious will come back positive to SARS-Cov-2. People who have had the disease up to 2 months prior may still have viral remnants that are amplified by high cycle rates, and generate positive results.

One problem with RNA viruses is that the RNA can be detected a long time after the person is no longer infectious, or even has active disease. The CDC recognised this in February 2021 and recommended PCR not be used to determine when isolation/quarantine should end.

Why does this matter? NSW currently uses RT-PCR tests at 40-45 cycles to:

  • perform mass population testing to identify and diagnose people with or without symptoms as being, or having been, infected with SARS-Cov-2 virus, and then putting them under controls like home quarantine or mandatory isolation NSW Health Department isolation requirements
  • diagnose the cause of a presenting patient’s respiratory illness as Covid-19
  • determine if a person diagnosed as having Covid-19 is infectious or likely to be infectious.

Diagnosis without symptoms does not conform to WHO guidelines. Diagnosis of respiratory illness as Covid with only a RT-PCR test risks error, depending on CT used. And infectivity is dependent on the CT selected, with >25-35 unlikely to be infectious.

This means the “active case” numbers reported daily are meaningless, as all or none could have been exposed to Covid up to 2 months earlier, all or none may be infectious, all or none could have active disease. It just isn’t clear, because CTs and reference ranges aren’t clear.

If the NSW Government and the Health Department were transparent and competent, they would report every positive case with the relevant details:

  • number of cycles required to generate a positive result relevant to lab reference ranges
  • presence or absence of symptoms
  • nature of symptoms
  • contact tracing information and epidemiological details.

After all, that is precisely what the WHO set out in its guidance from January 2021. PCR can’t be used alone in diagnosis, just as an aid:

Most PCR assays are indicated as an aid for diagnosis, therefore, health care providers must consider any result in combination with timing of sampling, specimen type, assay specifics, clinical observations, patient history, confirmed status of any contacts, and epidemiological information.

WHO Information Notice for Users 2020/05 [See also Version 1 ]

Revealing that information – particularly CT for necessary to reach a positive result – would reveal how many of the “active cases” are just artifacts of excessive cycles.

It can be done. From December 2020 Florida moved to require that labs report cycle thresholds and reference ranges for RT-PCR positives.

Put bluntly, RT-PCR tests weren’t designed to be used for mass testing separate from a presenting set of symptoms and broader considerations. The CDC stresses tests are likely to be accurate when two extra circumstances apply (pretest probability):

  • High prevalence in the group being tested (not apply in NSW or Australia)
  • Presence of symptoms and history of contact (ignored in NSW, which relies solely on PCR results).

Riders

Let’s not get too certain here. There are plenty of good scientific reasons to use higher cycle thresholds to identify specific information, or to understand more about what is happening.

Those reasons may exist. But we don’t know, because NSW Health is silent on the issues.

Be Careful Focusing on Exact Numbers of Cycle Thresholds

Comparable cycle thresholds can vary from lab to lab. It’s important not to try to lock in an exact number as an appropriate cycle threshold.

This isn’t nefarious. The same samples in different labs may need a different number of cycles to be positive, purely because of laboratory variation. It’s why there are laboratory-specific reference ranges for all pathology tests.

This makes it difficult to require publication of the threshold required for every positive test, since tests may be done in different labs. We need to have apples-apples. But there are ways to do it, and we should. It is relevant information.

Don’t Confound the April CDC Rule on Genomic Sequencing

In April 2021 the CDC issued controversial guidance on when Covid samples from vaccinated patients (breakthrough infections) should be submitted for genomic sequencing. That stated that only samples positive at =< 28 cycles should be submitted. This is not guidance on cycles for Covid positivity, and shouldn’t be confounded as such.

However, if genomic sequencing for vaccinated patients is only worth doing on =<28 cycle positive samples, what does that imply for CDC confidence in higher cycle thresholds in general? Did the CDC not want vaccinated false positives to be sequenced and reported? Not sure. The CDC subsequently took down the page, so no link. [secondary source]

NSW Health Won’t Explain and Doesn’t Want To

For the entire Covid pandemic NSW Health has been secretive, spin-driven and has obscured relevant data. That is continuing. Their silence on choice of RT-PCR Cycle thresholds, and the thresholds necessary for case positives, is in keeping with that.

Issues with over-cycling on PCR have been known for years. Its effect on false positives for Covid has been known since mid 2020. There is at least an issue requiring explanation.

The data is there. It reveals useful information. It can be provided. They won’t. They know they could be locking up people unnecessarily in quarantine or isolation. They know it’s likely they’re overcounting cases wildly. They don’t care.

And our media hasn’t asked a single question on cycle thresholds in 18 months.

And they wonder why there is a trust problem.


References: High Cycle PCR Tests, Infectivity and Viral Load

Viral load is a measure of both likelihood of active disease (being sick, with symptoms) and of infectivity. Infectivity requires a higher amount of virus than just being sick. The higher the CT is set, the less a PCR “positive” test means for likely disease or infectivity.

This is a problem for all of the different ways we use RT-PCR tests.

Infectivity

After a positive PCR test scientists can then test for live virus by trying to grow it in culture. When the cycle threshold is too high, it may come back as Covid-positive, but when scientists try to grow the virus, they can’t. That’s an indication of false positive. Note, only an indication, because you may have the disease but not be infectious (have virus that can grow in another person, or in culture). This is an important distinction and we shouldn’t confound the two.

A May 2020 research paper reports an attempt to grow the virus from RT-PCR positive samples with differing cycle thresholds.

They could only grow virus for positives that had cycle thresholds <25, and for samples taken within 8 days of the appearance of the first symptom. Note, however, they only had 90 samples with varying CTs, the median CT was 23, and the interquartile range of CT (chopping the top and bottom off the CT of the samples) was 17-32. Only 26/90 samples could grow virus in culture.

A followup to that paper notes some issues with using cell culture, but concludes:

Despite these limitations, the study by Bullard et al provides informative data on the period of infectivity of SARS-CoV-2, and helps to confirm that PCR positivity is likely not a reliable surrogate marker for determining the infectious status of COVID-19 patients. [my emphasis]

Similarly, in a recent letter to the Oxford Journal Clinical Infectious Diseases indicates <3% of positives with CT>35 result in positive cultures which indicate infectiousness. To be fair, for an extremely lethal disease <3% chance of infectivity may be an extreme risk. But Covid is not an extremely lethal disease.

In short, high cycle PCR testing (>25) is unlikely to be meaningful for determining infectivity.

An early August 2020 paper from the Oxford Centre for Evidence-Based Medicine puts it in a balanced, reasonable way. PCR tests just don’t tell us enough about disease or infectivity:

These studies provided limited data of variable quality that PCR results per se are unlikely to predict viral culture from human samples. Insufficient attention may have been paid how PCR results relate to disease. The relation with infectiousness is unclear and more data are needed on this.

If this is not understood, PCR results may lead to restrictions for large groups of people who do not present an infection risk.

The results indicate that viral RNA load cut-offs should be used: to understand who is infectious, the extent of any outbreak and for controlling transmission.

A December 2020 paper in Clinical Infectious Diseases reported in more detail about how higher CTs mean less virus and infectivity:

We included 29 studies reporting attempts at culturing, or observing tissue infection by, SARS-CoV-2 in sputum, nasopharyngeal or oropharyngeal, urine, stool, blood and environmental specimens. The quality of the studies was moderate with lack of standardised reporting. The data suggest a relationship between the time from onset of symptom to the timing of the specimen test, cycle threshold (Ct) and symptom severity. Twelve studies reported that Ct values were significantly lower and log copies higher in specimens producing live virus culture. Two studies reported the odds of live virus culture reduced by approximately 33% for every one unit increase in Ct. Six of eight studies reported detectable RNA for longer than 14 days but infectious potential declined after day 8 even among cases with ongoing high viral loads. Four studies reported viral culture from stool specimens…

Complete live viruses are necessary for transmission, not the fragments identified by PCR. Prospective routine testing of reference and culture specimens and their relationship to symptoms, signs and patient co-factors should be used to define the reliability of PCR for assessing infectious potential. Those with high cycle threshold are unlikely to have infectious potential. [my emphasis]

The earlier preprint of the same paper included stronger statements and the identification of problematic CT values (it’s unfair to quote a preprint after a peer-reviewed paper, but we need to see the sorts of values that are under debate):

…Five studies reported no growth in samples based on a Ct cut-off value. These values ranged from CT > 24 for no growth to Ct ? 34. Two studies report a strong relationship between Ct value and ability to recover infectious virus and that the odds of live virus culture reduced by 33% for every one unit increase in Ct. A cut-off RT-PCR Ct > 30 was associated with non-infectious samples...


Fauci on Cycle Thresholds above 35

These are quotes from a Tony Fauci interview at This Week In Virology, recorded July 17, 2020.

If you get a cycle threshold of 35 or more, the chances of it being replication-competent are miniscule…

You can almost never culture virus from a 37 threshold cycle…

I think if someone comes in with a 37, 38, even 36 cycles, you gotta just say, you know, it’s just dead nucleotides, period.

https://youtu.be/A867t1JbIrs

Reasons for false positives

In routine laboratory PCR testing, some false-positive results can be managed through standard curve or interim controls [35]. However, misleading results can occur due to: 1) inadequate laboratory rRT-PCR experience, 2) SARS-CoV-2 cross-contaminations, 3) detection of unspecified coronaviruses, 4) SARS-CoV-2 inactive/residual detections, 5) cross-reaction with nucleic acids from other pathogens or tissue cells, and 6) technical reasons relating to kit primers, probes and fluorescence type.

nih paper

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