“In June of 1944 Operation Titanic had 10 soldiers of the Allied Air Service parachute over the French countryside along with 500 “ruperts.” Ruperts were dummies, fabric stuffed with straw and sand tossed from the airplanes along with the soldiers. They were equipped with incendiary devices so that, upon impact, they ignited, leaving no trace that they were decoys.
It gave the illusion of an invasion far from where the actual invasion was taking place, which was Normandy. The Germans were duly deceived, diverted their resources, and this deception was decisive in making the Normandy invasion ultimately successful.
Intentional deceptions such as this have been part and parcel to warfare for centuries. These deceptions have often been the deciding factor in determining the outcome of battle.
The war against Covid-19 is no exception. Language around Covid-19 is infused with war metaphors. Time Magazine explains to us “Why the U.S. Is Losing the War on COVID-19,” while the NYTimes followed up to tell us “How America Lost the War on Covid-19.” In this war, as with Vietnam, we have two related “body counts” to help us understand just how badly we are losing to this viral enemy.
The first count is the cumulative deaths caused by Covid-19. The US recently crossed the “grim mile mark” of 200,000 deaths due to the disease. It is a tragic number of deaths, to be sure. But we can also be sure that, as an infectious disease, the cumulative number of deaths will certainly continue to rise into the indefinite future. No one knows what the efficacy will be of any future vaccine, but Dr. Fauci is hoping for at least 75%. In any case, there will always be unfortunate deaths to add to the cumulative death number. All infectious diseases, and in fact all potentially fatal diseases, are the same in this regard.
No one is anticipating complete eradication of Covid-19. This disease is expected to reach a background level, still infectious and occasionally deadly, but not epidemic. Cumulative deaths will continue to rise. The media will surely continue to toll that ominous bell because it carries the gravity of the situation like no other statistic.
The second count used by the media daily is “new cases.” These new cases are telling us just how rapidly this virus is disseminating through the population and is used as what we can expect as a surrogate marker for future deaths. Slowing the rise of new cases and squashing any “hotspots” and “outbreaks” of new case clusters is a prime motive behind essentially all social measures, e.g. mask mandates, social distancing, and business closures. For this reason, it is essential that we understand what a new case actually indicates. And to understand that, we first have to examine polymerase chain reaction (PCR), the laboratory technique used to diagnose a case.
PCR: The Basics
PCR is a technique for exponentially multiplying (“amplifying”) small pieces of DNA. DNA, recall, is made of a sequence of nucleotides that line up like beads on a string. PCR uses small, synthetic nucleotide strips called “primers” that bind to the target DNA, the piece to be amplified. These primers come in pairs and bind at pre-chosen regions on the target DNA at two locations that are relatively close to each other. The process of PCR is to replicate the strip of DNA between the two bound primers so that one initial copy becomes two. Run it through another cycle and the two copies become four. And so on.
SARS-CoV-2 is an RNA virus, not a DNA virus. To perform PCR on this virus it first has to be converted from a strand of RNA to a strand of DNA, a process called “reverse transcription.” The technique is thus abbreviated rtPCR.
Let’s say we don’t know if there is any target SARS-CoV-2 DNA in our sample of blood or, with Covid-19 testing, the sample is from a nasal swab. We place the swabbed sample in a solution, then we add the primers to that solution. If there is no target DNA in the sample, then it doesn’t bind to anything. Run through 40 cycles and there will still be no “signal” indicating that target DNA got amplified. That test is designated “negative.”
On the next sample suppose there is target DNA on the swab and so in the solution. Primers are added and bind to the target. Cycle, cycle, cycle 40 times. The signal appears, indicating that the target DNA was present in the sample all along. That sample has tested positive for Covid-19. Is the person infected with the virus? That is, after all, the important question we need to have answered.
PCR cannot possibly answer that question.
The full infectious genome of SARS-CoV-2 is approximately 30,000 nucleotides in length. If it is cut in half, for example, neither half will be able to carry out an infection. Only the full intact genome can carry out an infection. But when PCR is run, the target it seeks to amplify is not the full length of viral DNA. In fact it is not half or a quarter of the full DNA.
“Expected amplicon sizes of CDC assays are 72 bp, 67 bp,and 72 bp in length by the N1, N2,and N3, respectively.” .
N1, N2, and N3 indicate three different regions of the N gene, which the CDC picked as targets for PCR. It is noteworthy that the N1 and N2 targets are considered unique to SARS-CoV-2. The N3 target was intentionally picked because it is not unique to SARS-CoV-2, but “was designed to universally detect all currently recognized clade 2 and 3 viruses within the subgenus Sarbecovirus, including SARS-CoV-2, SARS-CoV, and bat- and civet-SARS–like CoVs.” 
Amplicon sizes of 72, 67, and 72 tells us that, when PCR is run according to CDC specifications, the three target DNA sequences are 72 nucleotides (“base pairs;” bp), 67 nucleotides, and 72 nucleotides. In other words, each target represents approximately 0.2% of the full viral genome, and adding up all three targets still represents just 0.7% of the full genome. If these three targets are found, how confident can we be that the other 99.3% of the genome needed to be an infectious viral particle is also present?
Apparently, not very.
The Center for Evidence-Based Medicine at Oxford University recently reviewed the evidence that a positive PCR test correlates to presence of infectious virus in the individual testing positive. Their conclusion was not encouraging:
“These studies provided limited data of variable quality that PCR results per se are unlikely to predict viral culture [i.e. infectious particles] 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.”
A more recent study confirmed the lack of correlation between infectious viral particles and PCR positivity. The study was to determine the extent to which ultraviolet irradiation of infectious viral particles impaired their ability to infect cells. Infectious viral particles of a known quantity were irradiated for different lengths of time. After each exposure two tests where run on those viral particles: one was a direct measure of how many infectious particles remained. The second was PCR to quantify how many “targets” were found in the sample.
Table 1 from that article has the telling data:
“It was clear something was awry when both the goats and the pawpaw tested positive for the coronavirus.” Source