Government of Ontario Confirms Westphalian Times Reporting on Cycle Thresholds

A new report by the Government of Ontario confirmed the findings of an investigative report by Westphalian Times about PCR testing and the occurrence of false positives due to high Ct values.

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A new report entitled “An Overview of Cycle Threshold Values and their Role in SARS-CoV-2 Real-Time PCR Test Interpretation” posted on Public Health Ontario’s website confirms what was reported in the Westphalian Times recent article about PCR test cycle thresholds

The report dated September 17, 2020 was posted on Public Health Ontario’s website over two weeks after The Westphalian Times began making inquiries about Ontario’s PCR cycle threshold (Ct) standards. The report was not provided to The Westphalian Times.

In our piece on PCR cycle thresholds, we found that in Canada the majority of COVID-19 test diagnostic standards may be too sensitive to reliably identify people currently suffering from COVID and thus detect and isolate those who are actually infectious. 

According to Public Health Ontario, high Ct values may result in false-positives being produced and the likelihood of having a false positive increase as the Ct level increases:

“The risk of false positive results increases as the pretest probability of COVID-19 decreases, such as in instances of low prevalence. Moreover, positive real-time reverse transcription (rRT)-PCR test results that are close to the limit of detection of an assay have a greater likelihood of being false positives.”

The report confirms WT reporting that labs have not been able to culture live virus from samples that only test positive with high cycle thresholds: 

“a study in which virus culture was performed at Canada’s National Microbiology Laboratory documented that specimens with Ct values > 24 were viral culture negative. ….the US CDC has reported that they were able to culture virus from specimens with Ct values up to the low 30s.” All of Canada’s labs use tests with cycle thresholds of at least Ct=35 and some as high as Ct=45 even though the report defines a high Ct as being 35 and greater.

Public Health Ontario goes on to confirm that “In general, specimens with Ct values well below the assay cut-off for positivity (e.g. Ct < 35 with the laboratory positivity cut-off for that assay set at Ct = 38) are less likely to be false positive.”  This confirms the point that the use of lower Ct’s results in fewer false positives.

The report discusses how positives with high Ct’s tend to typically be negative if the individual is retested:

“However, if the initial positive result was of high Ct value, near the assay cut-off, a repeat collection will typically be negative due either to lower viral shedding over time and/or inconsistent assay performance for specimens at or near the cut off.”

Again, the report discusses the importance of lower Ct values in determining true-positives in individuals who already had COVID-19 and continue to test positive after quarantine:

“To investigate whether a re-positive result is more likely to be ongoing detection from an original infection episode or a true new re-infection, the Ct value and number of targets detected may be helpful additions to the clinical context, and whether additional public health follow-up is necessary for a true re-infection. A re-positive value with lower Ct value (e.g., <32) would be required to conduct further analysis, such as viral genetic sequencing, to determine similarity to the original specimen or other cases that the re-positive individual was exposed to before the re-positive result.“

On July 30, Ontario’s Deputy Chief Medical Officer of Health Dr. Barbara Yaffe told the media:
“If you test somebody today, you only know if they’re infected today. In fact, if you are testing in a population that doesn’t have very much COVID, you’ll get false-positives almost half the time. That is, the person actually doesn’t have COVID, they have something else, they may have nothing.”

The Westphalian Times will continue to press other provincial health authorities on these issues.

Read our original piece here.

More to come.

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