High cases counts may not have justified ‘circuit breaker’

A COVID-19 warning sign on the Surrey-Langley border. The PCR test has been the yardstick with which we’ve measured this pandemic, but what how does the PCR test work? (Photo: Malin Jordan)A COVID-19 warning sign on the Surrey-Langley border. The PCR test has been the yardstick with which we’ve measured this pandemic, but what how does the PCR test work? (Photo: Malin Jordan)
Average daily deaths in B.C. for the first four months of calendar years 2014 to 2021. (Graphic: Canva)Average daily deaths in B.C. for the first four months of calendar years 2014 to 2021. (Graphic: Canva)
COVID-19 cases (in the 100s) and deaths per week in B.C. in 2021. (Graphic: Canva)COVID-19 cases (in the 100s) and deaths per week in B.C. in 2021. (Graphic: Canva)

As the province reopens at a snail’s pace, it’s worth looking back on how we spiraled into a renewed lockdown over the last eight weeks. Dr. Bonnie Henry used the hysteria of rising case counts to justify her “circuit breaker” March 29, even though deaths were declining.

And then Public Safety Minister Mike Farnworth and the province “doubled down” April 23 with an interregional travel ban when the data showed a flat fatality rate over a six-week period from March 21 to May 1 (from just before the circuit breaker through to the implementation of the travel ban), averaging 24.2 deaths per week (Epi-weeks 12-17).

Cases were up, but an increased death rate didn’t follow high case counts. (See charts above.) With cases peaking in week 14 (7,038), we should’ve seen deaths start to go up again in weeks 16 (31 deaths), 17 (16 deaths), and 18 (26 deaths).

If cases did predict impending deaths, case counts would be very useful. Without that, case counts just offer us a lot of fear and noise.

In the weeks before March 29, deaths dropped. Week 8 data (released March 10) revealed B.C. had 23 COVID deaths; week 9 data (released March 17), 24 deaths, and week 10 data (released March 24), 18 deaths. That was an average of 21.7 deaths per week over the period, but down from the 58.4 average over the first five weeks of 2021.

So if higher case counts do not reveal a worsening pandemic, what could be happening? And forget about citing an increase in vaccinations rates. As I wrote a few weeks ago, the death rate for B.C. has been stable: pre-pandemic, pandemic, pre-vaccine, post-vaccine. We are just not seeing any excess deaths in B.C. So as COVID deaths went up—or down—the average daily number of British Columbians that pass away has remained flat.

But to understand why cases skyrocketed, we need to pull back the curtain on COVID testing and understand how we get “cases” and what a “case” actually means. Rising case counts are the number one thing driving B.C.’s COVID response—and thus COVID fear.

THE PCR TEST

Cases of COVID-19 are found using the PCR test and it’s considered the gold-standard for COVID testing. But the PCR (polymerase chain reaction) test is anything but a “yes-no” answer to whether or not someone has COVID-19.

First, a health-care professional takes a swab, usually from the nose. This is then tested at the molecular level for SARS-CoV-2 (SCV2), that’s the virus that causes COVID. But SCV2 is an RNA virus, so the sample first has to be converted into DNA to be used in the PCR test. This process is called reverse transcription (rtPCR).

After converting the viral RNA (if present) into a DNA format, a lab tech attaches a primer-probe mix to the sample. The primer-probe also has a fluorescent molecule attached. This probe then “searches” for a specific part of the SCV2 genome. If it finds it, it attaches itself to the target area.

That “new” DNA, with the probe, is then copied over and over in a herculean bit of manufacturing on the molecular level: one becomes two, two becomes four, four becomes eight, and so on until repeated 30 (or more) times and you have billions of copies of the original sample. If the probe “attaches” to a very small part of the SCV2 genome, then it gets copied over and over along with the fluorescent molecule.

After each cycle, a PCR analyzer stimulates the sample with a laser, if a fluorescent molecule has bound itself to a part of the virus, then it will get amplified with the DNA sample. As the PCR analyzer “excites” the sample with that laser, the fluorescent molecule (if present) will emit light back at a specific wavelength. The analyzer will then determine if a positive sample is present.

But the SCV2 genome is made up of 29,903 base pairs.

Justine Ma, media relations for the Provincial Health Services Authority (PHSA), told the Cloverdale Reporter the B.C. CDC’s public health lab “targets RdRP and E genes as well as RNaseP for sample quality control” in their PCR tests.

“We have a network of cross-validated platforms such that testing across all BC laboratories are considered equivalent. Each of these assays have a slightly different chemistry and architecture.”

I asked her how much of the COVID genome’s 29,903 base pairs do PCR tests in B.C. test for?

“Unfortunately, we won’t have anyone available this week,” Ma wrote. “We have the information that we’ve provided and what’s available on the website. Thanks for your understanding.” Ma ignored requests from the Reporter to interview lab technicians and ignored subsequent emails asking to verify that specific question: which part is tested?

U.S. CDC

Jade Fulce, public affairs specialist with the U.S. CDC, told the Cloverdale Reporter that CDC testing kits have three primer-probe mixes that target two areas of the virus nucleocapsid, or N gene (2019-nCoV_N1 and 2019-nCoV_N2), and primer-probe mix that targets the human RNase P gene “for detection of human nucleic acids,” which is a control for sample integrity.

“The N1 target assay spans 71 bps in total, but only 67 base pairs are detected (2 bp gap between the F primer and probe and 2 bp gap between the reverse primer and probe),” Fulce wrote in an email. “The N2 target assay spans 66 bps in total but only 58 bp are detected (5 bp gap between the F primer and probe and 3 bp gap between reverse primer and probe).”

So the target assays for PCR tests from U.S. CDC kits search for 71 and 67 base pairs. That means their specific PCR test only looks for 138 base pairs out of a COVID genome that has 29,903 base pairs. That is 0.46 per cent of the COVID genome.

If we are testing a massive genome for less than 1 per cent of a virus, is it possible that positive tests could be the result of samples that have less than 100 per cent of the virus, so-called viral fragments?

This is significant because if a person is “infected” with a partial COVID genome they could pass along viral fragments to someone else, that viral fragment would not replicate in the newly “infected” person, and they wouldn’t get sick from the virus. Thus someone with a partial genome could be classified an asymptomatic carrier, as they’d test PCR positive.

Jonathan Jarry, a science communicator with the McGill Office for Science and Society, told the Reporter via telephone it’s possible for people to test positive if they have viral fragments in their body.

“At the tail end of the infection, it is being seen that people are no longer contagious, but they still have fragments of the virus in them. So that genetic material is picked up by the PCR test.”

Jarry worked in molecular diagnostics for years and has done countless PCR tests. He said he has never done a PCR for COVID-19, but he understands the technology fairly well.

“The PCR test was never meant to test for whether or not (a person) was infectious.”

He said to really figure out if a sample was infectious the sample would need to be grown in a laboratory to see if the virus would infect cells, only then would you know if the “PCR positive” test represented an actual infectious case.

“That requires a lot of time. The PCR test is much quicker,” Jarry explained. “It was never meant to test for infectivity, but it is the best surrogate for that kind of test.”

The B.C. CDC’s Public Health Laboratory confirmed B.C.’s case count is based on “PCR positive” cases.

“Culturing positive cases is not routinely used to diagnose COVID-19 in B.C.,” they lab noted via email.

CEBM

The U.K’s Oxford University Centre for Evidence-Based Medicine (CEBM) notes in an information page called “PCR positives: what do they mean?” that if a PCR test does find the COVID virus that “yes-no” question still remains. “Is the virus active, i.e. infectious, or virulent? The PCR alone cannot answer this question.”

Like Jarry, the CEBM says culturing the virus in a lab is the only way to find that out. “In viral culture, viruses are injected in the laboratory cell lines to see if they cause cell damage and death, thus releasing a whole set of new viruses that can go on to infect other cells.”

Jarry admits viral fragments could give positive PCR tests, but he thinks all positive PCR tests are representative of actual infectious cases of COVID-19, fully 100 per cent of the genome.

“Theoretically, I would agree with you, but it’s also a question of how many copies of the virus are there,” explained Jarry. “And sequencing the entire thing would be very expensive as well, whereas amplifying a part of it is a good [method].”

Without hearing back from Ma, or being granted access to a real person at the B.C. CDC, I don’t know how many base pairs B.C. labs are testing for. But it’s probably safe to infer they aren’t testing 29,903 base pairs.

SAMPPs

In a paper found on the database PubMed, a group of scientists hypothesized a scenario in which “PCR positive” cases may not be “positive” in the sense that it means an active case of COVID-19.

Titled “Is a COVID-19 vaccine developed by nature already at work?” the paper posits the idea virus fragments could account for rising case counts and plummeting death rates. “The COVID-19 positive cases are increasing at an alarming rate across the world. On the contrary, morbidity and mortality are showing a decreasing trend as time progresses.”

The authors says they were intrigued by the rise in asymptomatic cases which caused them to theorize that a “gradual development of immunity in the population” was occurring. “To date, no attention has been given to the accumulation of killed/inactivated/degenerated ‘SARS-CoV-2 associated molecular particle patterns’ (SAMPPs).”

The authors say there is a high possibility that SAMPPs exist because of the large size of the SCV2 genome and the way the virus is spread via respiratory droplets. “We hypothesized the existence of SAMPPs mediated the development of immunity against SARS-CoV-2 infection, which has caused an increase in the incidence rate of asymptomatic cases and a decrease in mortality rate.”

The whole paper offers an interesting read, but the main takeaway is that SAMPPs (killed/inactivated/degenerated virus fragments) offer the body an introduction to SCV2 and therefore create a “nature-made vaccine” that protects against the virus.

SAMPPs could also account for the high number of “PCR positive” cases. “The action of factors such as soaps, detergents, sanitizers or other spraying chemicals on SARS-CoV-2 leads to the formation of SAMPPs. SAMPPs are present on the inanimate objects and are present in abundance in COVID-19 affected areas of the community.”

To be sure, more study about SAMPPS is needed. But it helps to highlight a major concern with the polymerase chain reaction test being used as a diagnostic tool. If all samples are not cultured in the lab to determine infectivity, then how can we be sure a “PCR positive” case is an infectious case of COVID-19? If it isn’t, it’s possible we could be doing more harm than good by making non-infectious “PCR positive” subjects self-isolate.

CEBM

The Oxford University Centre for Evidence-Based Medicine also notes in their information page called “PCR positives: what do they mean?” that PCR detection of viruses is only helpful if the accuracy of the test can be understood. “It offers the capacity to detect RNA in minute quantities, but whether that RNA represents infectious virus may not be clear.”

The CEBM also notes they’ve found similarities in COVID data across various countries. “Our impression is that most data for all countries is in agreement with our interpretation, namely, PCR positives do not correlate to deaths in the future and are therefore meaningless, on their own, to interpret the spread of the virus in terms of potential deaths.”

It seems plausible then that “PCR positive” tests may be extending a pandemic that could be in our rearview mirror—that people with fragments of the virus, and not the full genome, are testing “PCR positive.” The PCR test, while effective, seems to be like using a nuclear bomb to take out a termite mound. I mean, yes, it’ll get the job done, but that’s a lot of force. Perhaps common sense needs to prevail over a highly technical test that could probably find a viral fragment in any sample.

Since “cases” began to skyrocket in about week 10, and since we haven’t seen a correlation to future deaths in the following nine weeks since that climb, and since we are not seeing any excess deaths (pre-or-post vaccine) above the average for B.C. (which I reported on last week), we need to figure out what exactly is happening. To me, it seems that “PCR positive” cases are up, but not cases of infectivity.

The next logical step is to stop focusing on case counts, as they clearly do not predict future deaths. Instead the government should just focus on death rates and ICU admissions. They are far better yardsticks with which to measure the pandemic. It’s time to stop using hysteria of case counts to determine our COVID response.

This is part two in a four-part series looking at our COVID response.

Read part one here: RETHINK: Are we following the right tack with our COVID response?

Read parts three and four in the coming weeks.

Editor’s note: this story has been updated to include information about the PCR analyzer and it has been shortened.



editor@cloverdalereporter.com

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