The PCR S Gene Dropout: Turning Failure Into A Positive

“The new Omicron VOC currently poses a detection challenge for diagnostic laboratories. At the moment there is uncertainty in the diagnostic performance of the available PCR assays, as all information obtainable at this early stage is based on companies’ in silico evaluations. For many of the systems, hardly any real-world evidence is available yet.”

https://smw.ch/article/doi/smw.2021.w30120

In order to comprehend the severity of the manipulation being perpetrated on the unsuspecting populace during this Testing Pandemic, it is important to understand the methods being utilized to pull off this deception. With the current rise of Omicron and the ensuing hysteria over what is essentially described as the common cold, an old trick is being employed to fool the gullible into believing a variant of a non-existent “virus” is running rampant and causing a massive spike in new cases. This sleight of hand is known as the S gene dropout, a failure in certain PCR tests to detect the “SARS-COV-2” S gene due to a deletion of amino acids H69 and V70 in the “virus” S gene. It is claimed that this deletion causes the failure of the PCR test to detect the S gene, otherwise known as the “spike” protein, which is a supposedly vital protein that is absolutely essential for infectivity. This is how Thermo Fischer, maker of the TaqPath PCR test mainly used for the detection of Omicron, describes the situation:

The S Gene Advantage

“The Applied Biosystems TaqPath COVID-19 diagnostic tests use a multi-target design, to compensate for emerging SARS-CoV-2 variants and mutations. Furthermore, the TaqPath tests are unique among the most commonly used molecular tests in that the multi-target design includes an S-gene target. The Omicron variant has been found to include the 69-70del mutation of the S gene, first identified as a mutation in the Alpha variant. This mutation causes a dropout of the S-gene target in results from widely used TaqPath COVID-19 Detection Kits. An S-gene failure does not mean a result is negative, only that the S gene was not detected. Multiple public health organizations have noted that this pattern of detection (i.e. S-gene dropout) can be used as marker for this variant, pending sequencing confirmation.”

https://www.thermofisher.com/blog/ask-a-scientist/the-s-gene-advantage-taqpath-covid-19-tests-early-identification-omicron-variant/

If the S gene is not detected, this should signal that this gene is not present at all in the sample. This should mean that there is no spike protein on Omicron. Maybe this would be why recently aquired images of particles assumed to be Omicron contain no spikes whatsoever.

However, due to genomic analysis of the spike protein, researchers decided that there is a mutation on the spike protein which allows it to evade detection. Thus, even though this is a failure of the PCR test to detect the most vital part of the “virus” which it theoretically uses to gain entry into a cell to hijack the cells machinery in order to make more copies of itself, researchers claim that it is not a fault in the test per se but that this is in fact a way to detect Omicron from amongst the many variants currently circulating.

While this nifty little S gene trick seems like a surefire way to catch the mysterious Omicron in action, there are some major reasons not to trust any of the claims made about Omicron regarding PCR results gained in this way. For starters, let’s see what the WHO has on this dropout:

Enhancing readiness for Omicron (B.1.1.529): Technical brief and priority actions for Member States

“The diagnostic accuracy of routinely used PCR and antigen-based rapid diagnostic test (Ag-RDT) assays does not appear to be impacted by Omicron; studies of the comparative sensitivity of Ag-RDTs are ongoing. Most Omicron variant sequences reported include a deletion in the S gene, which can cause an S gene target failure (SGTF) in some PCR assays. Although a minority of publicly shared sequences lack this deletion, SGTF can be used as a proxy marker to screen for Omicron. However, confirmation should be obtained by sequencing, since this deletion can also be found in other VOCs (e.g. Alpha and subsets of Gamma and Delta) that are circulating at low frequencies worldwide.”

“Because SGTF from commercial PCR kits is indicative for Omicron, it can be used as a proxy marker for this variant. However, it should be noted that a small minority of Omicron sequences lack this deletion and will be missed by this screening method.”

“The Omicron variant includes Pango lineages B.1.1.529, BA.1, BA.2 and BA.3. BA.1, which accounts for 99% of sequences submitted to GISAID as of 23 December, and BA.3 have the 69-70 deletion in the spike protein, while BA.2 does not. Knowledge of B.1.1.529 is still developing, but this lineage is more diverse, with the 69-70 deletion present in about half of all currently available sequences.

Presence of the 69-70 deletion in the spike protein causes a negative signal for the S gene target in certain PCR assays. This S-gene target failure (SGTF) can be used as a marker suggestive of Omicron. However, confirmation should be obtained by sequencing for at least a subset of samples, because this deletion is found in other VOCs (e.g. Alpha and subsets of Gamma and Delta), which are circulating at low levels worldwide.”

https://www.who.int/publications/m/item/enhancing-readiness-for-omicron-(b.1.1.529)-technical-brief-and-priority-actions-for-member-states

It would seem that according to the WHO, even though the S gene dropout can be used as a marker suggestive of Omicron, the deletion that triggers this failure is only found in about half of the sequenced samples. They admit that some screenings using this dropout method will “miss” Omicron as those copies apparently do not possess this spike protein mutation. The WHO also admits that this deletion and the resulting S gene dropout are not specific to Omicron and can be found in Alpha, Gamma, and even Delta. Despite this, the WHO still recommends using the S gene dropout as a suggestive surrogate marker for a variant of a non-existent “virus.”

Maybe the FDA will disagree with the WHO’s assessment? Let’s take a look at a recent release of theirs on this topic to see what can be uncovered:

SARS-CoV-2 Viral Mutations: Impact on COVID-19 Tests

Genetic Variations: Background and Considerations

“A mutation (also referred to as viral mutation or genetic mutation) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus is a change in the genetic sequence of the SARS-CoV-2 virus when compared with a reference sequence such as Wuhan-Hu1 (the first genetic sequence identified) or USA-WA1/2020 (the first identified in the United States). A new variant (virus variant or genetic variant) or sub-lineage of SARS-CoV-2 may have one or more mutations that differentiate it from the reference sequences or predominant virus variants already circulating in the population.”

“The presence of mutations in the SARS-CoV-2 virus in a patient sample can potentially impact test performance. The impact of mutations on a test’s performance is influenced by several factors, including the sequence of the variant, the design of the test, and the prevalence of the variant in the population.”

Omicron Variant: Impact on Molecular Tests (As of 12/22/2021) 

“The FDA’s analysis to date has identified certain EUA-authorized molecular tests whose performance may be impacted by mutations in the SARS-CoV-2 omicron variant. These tests fall into two categories, as described below: those that are expected to fail to detect the SARS-CoV-2 omicron variant, and those that are expected to detect the SARS-CoV-2 omicron variant with a specific gene drop out detection pattern.”

“Potential Impact: Since these tests are designed to detect multiple genetic targets, the overall test sensitivity should not be impacted. The pattern of SARS-CoV-2 detection with one gene drop out may provide a signal that the omicron variant may be present so that sequencing can be considered to characterize the variant. However, testing positive for SARS-CoV-2 with one of these tests does not mean an individual is infected with the omicron variant. Further, not all patient samples with the omicron variant display a mutation that leads to a gene drop out. Therefore, the omicron variant may still be present without a gene drop out detection pattern.”

Recommendations for Clinical Laboratory Staff and Health Care Providers Using These Tests

• “Be aware that the target failure or gene drop out pattern of detection (reduced sensitivity with the one genetic target) when using these tests is consistent with certain mutations, including those in some samples of the omicron variant. If a laboratory reports a gene drop out detection pattern when providing test results, we encourage laboratories to explain what the pattern may or may not mean.
• A gene drop out may occur due to different mutations in other variants and may not be specific to the omicron variant. A gene drop out may also be observed without the presence of a mutation in the target area, due to the sensitivity of the genetic target. Therefore, the presence of a gene drop out detection pattern is not a definitive confirmation of the presence of the omicron variant.
• The presence of a gene drop out detection pattern can signal that sequencing should be considered to characterize the variant in that specimen.
• N-gene and S-gene drop outs are typically not observed in the delta variant. Specimens with a gene drop out detection pattern may be omicron variants and should be prioritized for sequencing confirmation.”

https://www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/sars-cov-2-viral-mutations-impact-covid-19-tests

According to the FDA, while they have identified and authorized the use of PCR tests affected by the S gene dropout to be used as a proxy for Omicron, this gene failure is not specific to Omicron and is found in other variants. In other words, this is a completely non-specific reaction that can not differentiate between variants even though it is being used as such. Like the WHO, the FDA states that this spike protein mutation, along with the subsequent dropout, are not found in all cases of Omicron. If one does test positive for “SARS-COV-2” based on the S gene dropout, it does it not mean they are infected with Omicron and Omicron may still be present in positive tests without the S gene dropout. This dropout may still occur even if this mutation in the spike protein is not present in the sequence. Basically, if we are to take the FDA at their word, the PCR results (irregardless of the S gene dropout) are utterly meaningless.

It would seem that both the WHO and FDA are in agreement that this non-specific testing failure can be used as a proxy for the variant of a non-existent “virus.” Regardless, it is becoming clearer that this dropout isn’t the indicator these organizations were hoping it to be despite their claims to the contrary. Perhaps the CDC will help to clear up the inherent contradiction of both the WHO and FDA claiming a specific response from a non-specific PCR (non)reaction:

“To accelerate detection of COVID-19 cases attributed to the Omicron variant until they are common enough to be reliably measured by routine genomic surveillance, enhanced surveillance was initiated through National SARS-CoV-2 Strain Surveillance on November 28. The method is based on rapid screening for S-gene target failures (SGTFs) by polymerase chain reaction (PCR)–based diagnostic assays to flag potential cases of Omicron variant infection for confirmation by genomic sequencing (5). Specimens that display SGTFs have a higher likelihood to be Omicron (although SGTFs are not unique to Omicron) based on a mutation (69–70 deletion) that reduces S-gene target amplification in some PCR assays.”

https://www.cdc.gov/mmwr/volumes/70/wr/mm7050e1.htm

“SGTF has been observed in other variants and thus is not specific to the Omicron variant. SGTF has also been observed without the presence of a mutation in the S gene, due to the sensitivity of the S-gene target. Therefore, these tests cannot be used as a diagnostic tool or specific identifier of the Omicron variant.

SGTF is not typically observed in the Delta variant. Since Delta is the primary variant circulating in the United States, specimens with an SGTF profile may be potentially Omicron variants and should be prioritized for sequencing confirmation.”

“Results regarding the presence of the Omicron variant, or any other variant, should not be reported back to patients or providers and cannot be used for diagnostic purposes.”

https://www.cdc.gov/csels/dls/locs/2021/12-03-2021-lab-alert-CDC_Update_SARS-CoV-2_Omicron_Variant.html

It appears that the CDC wholeheartedly agrees with both the WHO and the FDA regarding the lack of uniqueness and non-specificity of the S gene dropout in regards to Omicron, the fact that these dropouts occur without any spike protein mutations whatsoever, and that these dropouts can occur with Delta. However, despite knowing all of this, the CDC still recommends using this non-specific testing failure in order to accelerate the detection (and cases) associated with Omicron. They even go so far as to state that results should not be given to patients nor providers and that they can not be used for diagnosis. Why the secrecy CDC?

It should be pretty clear that this S gene deopout trick is essentially useless. However, if the contradictory information from the WHO, FDA, and the CDC were not convincing enough, maybe the “stealth” Omicron variant will be? Apparently early on, researchers decided to split Omicron into two distinct sub-lineages of the same variant: BA.1 and BA.2. They were split due to the fact that there were Omicron sequences with the spike protein deletion (BA.1) and those that were sequenced without the deletion (BA.2). Obviously, this means while Omicron can be “detected” by the S gene dropout, it also can not be “detected” by the S gene dropout as previously stated by all three organizations:

Scientists find ‘stealth’ version of Omicron that may be harder to track

“Scientists say they have identified a “stealth” version of Omicron that cannot be distinguished from other variants using the PCR tests that public health officials deploy to gain a quick picture of its spread around the world.

The finding came as the number of cases of the original Omicron variant detected in the UK rose by 101 to 437 in a single day and Scotland announced a return to working from home.

The stealth variant has many mutations in common with standard Omicron, but it lacks a particular genetic change that allows lab-based PCR tests to be used as a rough and ready means of flagging up probable cases.

The variant is still detected as coronavirus by all the usual tests, and can be identified as the Omicron variant through genomic testing, but probable cases are not flagged up by routine PCR tests that give quicker results.

Researchers say it is too early to know whether the new form of Omicron will spread in the same way as the standard Omicron variant, but that the “stealthy” version is genetically distinct and so may behave differently.”

“There are two lineages within Omicron, BA.1 and BA.2, that are quite differentiated genetically,” Prof Francois Balloux, the director of the University College London Genetics Institute, said. “The two lineages may behave differently.”

Scientists use whole genome analysis to confirm which variant has caused a Covid infection, but PCR tests can sometimes give an indication. About half of the PCR machines in the UK look for three genes in the virus, but Omicron (and the Alpha variant before it) test positive on only two of them. This is because Omicron, like Alpha, has a genetic change called a deletion in the “S” or spike gene. The glitch means that PCR tests that display so-called “S gene target failure” are highly suggestive of Omicron infections.

Informally, some researchers are calling the new variant “stealth Omicron” because it lacks the deletion that allows PCR tests to spot it.

One major unknown is how the new variant emerged. While it falls under Omicron, it is so genetically distinct that it may qualify as a new “variant of concern” if it spreads rapidly. To have two variants, BA.1 and BA.2, arise in quick succession with shared mutations is “worrying” according to one researcher, and suggests public health surveillance “is missing a big piece of the puzzle.”

https://www.google.com/amp/s/amp.theguardian.com/world/2021/dec/07/scientists-find-stealth-version-of-omicron-not-identifiable-with-pcr-test-covid-variant

We are to believe that the S gene dropout is a surrogate marker for Omicron and is being used to accurately depict the fast spread of this “highly transmissible variant.” However, it is repeatedly admitted that the dropout is not specific to Omicron and that not all cases of Omicron are detected using this method as not all Omicron sequences are identical. Thus, Omicron was divided into those sequences that have this deletion and those that don’t. This means that the S gene dropout will work for Omicron but it also won’t. This seems like an obvious case of the Big Three trying to have their cake and eat it too.

Noticing this blatant contradiction, a few researchers wrote an open letter in the BMJ calling for better testing methods to detect this and future “variants of concern:”

We need increased targeted measures now to slow the spread of omicron

“Therefore, SGTF during RT-PCR with kits that detect the S-gene has been used as a proxy test for the Omicron variant pending sequencing confirmation. Moreover, because several nations currently lack sufficient sequencing capacity, SGTF has been employed to screen suspected Omicron cases for WGS. The SGTF growth rate, which was used with the Alpha variant [5], can serve as a suitable surrogate for the level of Omicron community transmission.

However, the SARS-CoV-2 Omicron (B.1.159) lineage is now being proposed to be split into two sub-lineages: BA.1 and BA.2.

While both lineages share a number of common defining mutations and appear to be co-circulating, the new recognised BA.2 sub-lineage does not carry the Spike del69-70 mutation which may hinder the use of commercially available PCR tests to diagnose Omicron based on “S-gene target failure”.[8,9]

In fact, recently sequenced cases belonging to the BA.2 sub-lineage have not been flagged by the aforementioned SGTF approach.[9]

Therefore, apart from the WHO’s recommendation that a subset of SARS-CoV-2 confirmed cases be sampled for WGS, cases from unique transmission episodes, unexpected disease presentation or severity, vaccination breakthrough, critically ill patients, and overseas travellers should all be included, subject to local sequencing capacity.[1]

More importantly, Governments across the world will need to optimize the RT-PCR kits and their supply chain and adopt a balanced sampling strategy for WGS to confirm the B.1.1.529 variant.

In brief, although SGTF represents an effective testing strategy to contain Omicron through targeted contact tracing and isolation, the rapid evolution of the variants and the unfolding data regarding their genetic profile needs to be fully incorporated into the diagnostics tools if we are to succeed in our quest to conquer the idiosyncrasies of SARS-CoV-2.”

https://www.bmj.com/content/375/bmj.n3133/rr

While it is a good suggestion by the researchers not to rely on a non-specific S gene dropout and small-scale limited genomic sequencing to confirm the existence and spread of any variant, creating improved diagnostic tools with increased testing/sequencing of a greater number of people is definitely not the answer. This is especially true when the S gene dropout has been shown in the past to be an unreliable diagnostic tool. A study from April 2021 highlighted some of the flaws with relying on a testing failure to determine disease prevalence. Beyond the problems with relying on the S gene dropout already outlined by the WHO, FDA, and CDC,this study reported that the SGTF has issues with false and spurious (i.e. fake) results and can be misleading:

Reliability of Spike Gene Target Failure for ascertaining SARS-CoV-2 lineage B.1.1.7 prevalence in a hospital setting

“SGTF has been used to identify lineage B.1.1.7 in the community and forms the basis for many studies looking at its transmission and severity [1,4–6]. Our data suggest that both false positive and false negatives can occur which may skew the positive predictive value of SGTF. In this study, lineage B.1.258, which also carries the spike deletion 69/70, was prevalent locally and we observed false positive lineage B.1.1.7 calls in 9.6% of cases. The incidence of false positives decreased as the more transmissible B.1.1.7 outcompeted B.1.258. By week 51 more than 90% of SGTF was B.1.1.7 (Figure S2).

We also found that there is a risk that spurious S gene results may be observed (as was the case with one of the assays used) and without careful review and consideration of the PCR results the prevalence of SGTF (and consequently lineage B.1.1.7) may be underestimated. This could be due to imperfect colour compensation on qPCR machines other than those made by the manufacturer of the assay, further complicated by the lack of controls for each single target of the multiplex assay to check for colour bleedthrough. The qPCR data from the manufacturer’s machine is also interpreted by separated software developed by the manufacturer and it is unclear how thresholding is performed and how the software handles any noise or curves that do not have an exponential shape.

This phenomenon is evidently dependent on the PCR machine and dyes used. This is reflected in the fact that the false negative results are restricted to just one of the two sites studied (one site used the manufacturer’s qPCR machine, the other a different machine with colour compensation performed with the manufacturer’s calibration plates).

While this phenomenon was only observed in one of the two set of samples analysed here, it has also been independently observed for lineage B.1.1.7 and SGTF in Portugal. [7]. Additionally, a locally developed assay that mimicked SGTF with a different dye did not show the same behaviour (data not shown).

Thus, in summary, SGTF is an important surrogate marker for the VOC 202012/01, and useful for large scale epidemiology studies. However, care needs to be taken where sample numbers are small, for example in care homes or hospitals for example where the intention is to link lineage B.1.1.7 to outcomes or in scenarios where lineage B.1.1.7 variants are in the minority. In these cases, the use of SGTF can be misleading and sequencing is recommended.”

https://www.medrxiv.org/content/10.1101/2021.04.12.21255084v1.full

In Summary:

• According to Thermo Fisher, the TaqPath tests are unique among the most commonly used molecular tests in that the multi-target design includes an S-gene target
• The Omicron variant has been found to include the 69-70del mutation of the S gene, first identified as a mutation in the Alpha variant
• This mutation causes a dropout of the S-gene target in results from widely used TaqPath COVID-19 Detection Kits
• An S-gene failure does not mean a result is negative, only that the S gene was not detected
• Multiple public health organizations have noted that this pattern of detection (i.e. S-gene dropout) can be used as marker for this variant, pending sequencing confirmation
• According to the WHO, most Omicron variant sequences reported include a deletion in the S gene, which can cause an S gene target failure (SGTF) in some PCR assays
• Although a minority of publicly shared sequences lack this deletion, SGTF can be used as a proxy marker to screen for Omicron
• However, confirmation should be obtained by sequencing, since this deletion can also be found in other VOCs (e.g. Alpha and subsets of Gamma and Delta) that are circulating at low frequencies worldwide
• It should be noted that a small minority of Omicron sequences lack this deletion and will be missed by this screening method
• Knowledge of B.1.1.529 is still developing, but this lineage is more diverse, with the 69-70 deletion present in about half of all currently available sequences
• This S-gene target failure (SGTF) can be used as a marker suggestive of Omicron
• According to the FDA, a mutation (also referred to as “viral” mutation or genetic mutation) of the severe acute respiratory syndrome “coronavirus 2 virus” is a change in the genetic sequence of the “SARS-CoV-2 virus” when compared with a reference sequence such as Wuhan-Hu1 (the first genetic sequence identified) or USA-WA1/2020 (the first identified in the United States)
• The impact of mutations on a test’s performance is influenced by several factors:
  1. The sequence of the variant
  2. The design of the test
  3. The prevalence of the variant in the population
• The FDA categorized tests into two categories:
  1. Those that are expected to fail to detect the “SARS-CoV-2” omicron variant
  2. Those that are expected to detect the “SARS-CoV-2” omicron variant with a specific gene drop out detection pattern
• They claim that this pattern of “SARS-CoV-2” detection with one gene drop out may provide a signal that the omicron variant may be present so that sequencing can be considered to characterize the variant
• However, testing positive for “SARS-CoV-2” with one of these tests does not mean an individual is infected with the omicron variant
• Further, not all patient samples with the omicron variant display a mutation that leads to a gene drop out
• Therefore, the omicron variant may still be present without a gene drop out detection pattern
• A gene drop out may occur due to different mutations in other variants and may not be specific to the omicron variant
• A gene drop out may also be observed without the presence of a mutation in the target area, due to the sensitivity of the genetic target
• Therefore, the presence of a gene drop out detection pattern is not a definitive confirmation of the presence of the omicron variant
• The presence of a gene drop out detection pattern can signal that sequencing should be considered (but not required) to characterize the variant in that specimen
• N-gene and S-gene drop outs are typically (i.e. in most cases; usually) not observed in the delta variant (in other words, they can occur in Delta)
• According to the CDC, in order to accelerate detection of “COVID-19” cases attributed to the Omicron variant until they are common enough to be reliably measured by routine genomic surveillance, the PCR S gene dropout was employed
• Specimens that display SGTFs have a higher likelihood to be Omicron (although SGTFs are not unique to Omicron) based on a mutation (69–70 deletion) that reduces S-gene target amplification in some PCR assays
• SGTF has been observed in other variants and thus is not specific to the Omicron variant
• SGTF has also been observed without the presence of a mutation in the S gene, due to the sensitivity of the S-gene target
• Therefore, these tests cannot be used as a diagnostic tool or specific identifier of the Omicron variant
• SGTF is not typically observed in the Delta variant (again with that word “typically”)
• Since Delta is the primary variant circulating in the United States, specimens with an SGTF profile may be potentially Omicron variants and should be prioritized for sequencing confirmation
• Results regarding the presence of the Omicron variant, or any other variant, should not be reported back to patients or providers and cannot be used for diagnostic purposes (why so secretive…?)
• Scientists say they have identified a “stealth” version of Omicron that cannot be distinguished from other variants using the PCR tests that public health officials deploy to gain a quick picture of its spread around the world
• The “stealth” variant lacks a particular genetic change that allows lab-based PCR tests to be used as a rough and ready means of flagging up probable cases
• The “stealthy” version is genetically distinct and so may behave differently
• There are two lineages within Omicron, BA.1 and BA.2, that are quite differentiated genetically
• While it falls under Omicron, it is so genetically distinct that it may qualify as a new “variant of concern” if it spreads rapidly
• Several researchers wrote an open letter in the BMJ addressing their concerns regarding testing for variants
• Because several nations currently lack sufficient sequencing capacity, SGTF has been employed to screen suspected Omicron cases for WGS
• The SGTF growth rate, which was used with the Alpha variant, can serve as a suitable surrogate for the level of Omicron community transmission (how convenient…)
• While both lineages share a number of common defining mutations and appear to be co-circulating, the new recognised BA.2 sub-lineage does not carry the Spike del69-70 mutation which may hinder the use of commercially available PCR tests to diagnose Omicron based on “S-gene target failure”
• In fact, recently sequenced cases belonging to the BA.2 sub-lineage have not been flagged by the aforementioned SGTF approach
• The researchers state that apart from the WHO’s recommendation that a subset of “SARS-CoV-2” confirmed cases be sampled for WGS, cases from unique transmission episodes, unexpected disease presentation or severity, vaccination breakthrough, critically ill patients, and overseas travellers should all be included, subject to local sequencing capacity
• They concluded that although SGTF represents an effective testing strategy to contain Omicron through targeted contact tracing and isolation, the rapid evolution of the variants and the unfolding data regarding their genetic profile needs to be fully incorporated into the diagnostics tools if they are to succeed in the quest to conquer the idiosyncrasies of “SARS-CoV-2”
• In an April 2021 study, researchers found that their data suggested that both false positive and false negatives can occur which may skew the positive predictive value of SGTF
• In this study, lineage B.1.258, which also carries the spike deletion 69/70, was prevalent locally and they observed false positive lineage B.1.1.7 calls in 9.6% of cases (in other words, they mixed up their variants using the S gene dropout)
• They also found that there is a risk that spurious (i.e. fake) S gene results may be observed (as was the case with one of the assays used) and without careful review and consideration of the PCR results the prevalence of SGTF (and consequently lineage B.1.1.7) may be underestimated (granted, they are assuming SGTF results = B.1.1.7)
• Reasons for spurious results include:
  1. Imperfect colour compensation on qPCR machines other than those made by the manufacturer of the assay
  2. Complications by the lack of controls for each single target of the multiplex assay to check for colour bleedthrough
  3. The qPCR data from the manufacturer’s machine is interpreted by separated software developed by the manufacturer and it is unclear how thresholding is performed and how the software handles any noise or curves that do not have an exponential shape
• The researchers concluded that care needs to be taken where sample numbers are small, for example in care homes or hospitals for example where the intention is to link lineage B.1.1.7 to outcomes or in scenarios where lineage B.1.1.7 variants are in the minority
• In these cases, the use of SGTF can be misleading and sequencing is recommended

While there are numerous reasons not to trust any of the information coming out from these pharmaceutically-controlled organizations, (such as the actual lack of any purified/isolated particles claimed to be “SARS-COV-2”) the engine driving this Testing Pandemic is the misuse, misinterpretation, and abuse of PCR. The use of the PCR S gene dropout is a cheat code for accelerating the narrative of increasing case numbers. It is being used as a proxy for Omicron cases yet it is not specific to the Omicron variant and was found to occur in Alpha, Gamma, and even the Delta variants. The 69/70 deletion in the spike protein, which is supposed to be a defining characteristic of Omicron and is claimed to cause this dropout, is not even found in all sequences of the variant. In fact, it is only found in about 50% of the sequences. Thus, Omicron was split into two sub-lineages: those that have the deletion and can cause the S gene dropout, and those that do not. Due to this lack of specificity and the variance is the 69/70 deletion, even if a test is determined positive using the S gene dropout, this does not mean one is infected with Omicron and a positive test without an S gene dropout could still be considered Omicron based on sequencing.

Whatever the tests may show, according to the CDC, the results should not be shared with patients nor their providers and can not be used for diagnosis. This should make it extremely clear that not only is the S gene dropout an absolutely useless measure, the PCR test results are worthless as well. The S gene dropout is just another trick up the sleeve of these criminals that is used to continue to pull the wool over the eyes of the gullible in order to sell the idea of a new highly transmissible variant for a non-existent “virus.” Don’t fall for it.