Recently, I filed another Freedom of Information Request with the Province, specifically the NS Health Authority, asking for several pieces of information regarding PCR testing since April 1, 2021. The information I requested was as follows:
- I would like an updated version of the document including any changes to the cycle threshold for each lab in NS for all tests performed in the updated date range (April 1 2021 to present). What is the average number of PCR amplification cycles that has been required to determine a positive Covid-19 test in Nova Scotia to date, since April 1 2021?
- Of the total positive Covid-19 tests in NS to date (approximately 3978 since April 1 2021), how many (or what percentage) of them fit into the following PCR cycle threshold ranges? <20, 20-25, 25-30, 30-35, >35
- Is the cycle threshold used to test a Vaccinated vs Unvaccinated person any different?
Here is the initial reply I had:
"We only have 5% of the data readily available to be reported on at this time. 52% of data has information available in the comment field, but the information has to be manually extracted and entered into a reportable field. For the remaining tests, we would have to access the instrument data to pull out the cycle threshold value, if the information is even there. If you are willing to take the data that we do not need to retrieve then there may not be a fee."
What this means is, of the 3000+ PCR tests I was inquiring about, only 52% had the data available at all, but only 5% were recorded in the appropriate field. In order to get beyond 5% of the data, I was delivered an invoice in the amount of $3570 to cover 120 hours of billable time, beyond the "free" 2 hours that comes with any freedom of information request. The reason for the lack of data available this time, when it was readily available for my previous request (data from March 2020 to March 2021) was given as follows:
"Cycle threshold values need to be recorded manually, they are not automatically added to the laboratory information system. NS Health was recording them prospectively principally for the purposes of downstream surveillance testing i.e. qualification for genomic sequencing. NS Health was better able to support this activity during earlier waves with low numbers of positives over a longer timeframe. This process of recording those values was greatly reduced in the third wave to support clinical diagnostic COVID-19 testing and other case management activities with public health. A backlog of compiling cycle threshold values if they are still available now exists, however, because we have changed our downstream surveillance approach to sequence only a sub-set of the positives we are not intending to go back and record all of the cycle threshold values for all of the positives in the third wave."
Basically, they recorded this data for each test prior to the third wave, but now don't. The above reference to sequencing relates to genome sequencing. This is the process why which a positive test sample is shown to be infectious, or not. As in, if they are able to sequence the virus from the sample, then it would be deemed infectious, otherwise not. This is what Manitoba's chief microbiologist was referring to when under oath in court recently, when he stated that he has never been able to sequence the virus when the sample came from a test as 25 or greater PCR cycles. He also stated that he has only been able to sequence 44% if positive tests when a PCR cycle threshold of 18.
I currently have a request in with the freedom of information office to determine what data is readily available regarding genome sequencing in NS, as that would actually be the best data to get to truly understand the nature of testing and infectiousness in NS.
With all that said, I did opt to have my initial request fulfilled using the 5% of data they had readily available. As a result, its not possible to infer if this is a fair assessment of the remaining 95% of data that I don't have, or not. This is because I am unsure as to how they selected the 5% of tests they reported the cycle threshold on. It could be random or it could be very specific. So the data I am about to provide, doesn't allow many conclusions to be drawn as we simply don't have the information required to know whether or not this 5% is representative of the remaining 95% or not.
Here are the answers to my initial request:
The labs appear to be operating the same as they were during my first request back in March 2021 (available HERE). The new data above shows that they are using a cycle threshold of 45, but a test is only deemed positive if it reaches a positive result by cycle 34, 36 or 37 depending on the lab. Any positive result above those thresholds will be deemed an indeterminate test.
In my request from March 2021, the average positive occurred at a cycle count of 26.9, with 35% of positive results occurring at greater than 30 cycles. Based on the 307 positive test results included here (5% of the total, remember), 36.2% occurred at less than 2 cycles and just 9.4% at greater than 30 cycles. However, I can't stress enough that this data cannot be compared to my initial request from March because we do not know if this 5% is representative of the missing 95%. Unfortunately, this just doesn't tell us much of anything.
The province also confirmed that:
"The cycle threshold used to test a vaccinated and unvaccinated person is not different."
In conclusion, we know that vaccination status isn't a factor in how testing is being performed, and we know that the labs thresholds were not altered for the "3rd wave". What we don't know, since we can't infer from the 5% data given, is at what cycle most people were testing positive at. Hopefully I'll be able to get some genome sequencing data before long, which could prove incredibly interesting.
Some final context, we know unequivocally (link) that at 30 cycles, 80% of positive test results are "dead", non-infectious viral material, aka, meaningless, not a case, not anything worth discussing. At 35 cycles, this becomes 97% and beyond 35, it's effectively 100% of positive results are "false".
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