We Americans have a long and glorious history of snake oil salesmen. There is always someone peddling useless — and sometimes harmful — concoctions when there’s sickness and suffering. John D. Rockefeller’s father was just such an itinerant quack. What finer pedigree could you ask for?

It should be no surprise then that here in the US of A, we’ve taken the most dubious claims of hydroxychloroquine’s effects on COVID-19 and hyped them from the highest podium in the land: “What do you have to lose?”.

Aside from the shame of snake oil salesmen being encoded into the DNA of our country is the fact that Americans always seem eager to buy what the shameless hucksters are selling.

And then, there’s the question of the snake oil itself. The stuff in the bottle. What is it anyway?

What is hydroxychloroquine, and where does it come from?

The short answer is that hydroxychloroquine is a modification of an earlier drug called chloroquine, which in turn is a synthetic version of a natural drug derived from tree bark that many of us have heard of, called quinine. Quinine has a veeery long history as an antimalarial drug. Still, it is also commonly known as an additive in tonic water (as in gin and tonic), giving it its characteristic bitter taste. Quinine is a plant alkaloid. Alkaloids can be toxic and are known for their bitterness. Think of caffeine — a classic alkaloid.

With some very smart commentators blogging on current issues with these drugs (Derek Lowe on the Science Magazine website is particularly good).

Despite the fun of digging into that black hole of technical information, I thought the back story was even more interesting.

Countess Ana de Osorio

It all starts with Ana de Osorio, wife of Luis Jeronimo de Cabrera, Count of Chinchon and importantly, Viceroy of Peru from 1629 to 1639.

I love the names and titles.

Ana de Osorio, Countess of Chinchon…

In 1638, the story goes, Ana de Osorio became very sick from malaria. The governor of Loxa wrote to the viceroy claiming to have been cured by the bark of the quinaquina tree. The governor was summoned, the medicine administered, and Ana was cured. Ana returned soon after to Spain bringing this miraculous bark of the tree eventually named after her as the Cinchona tree.

It turns out that this story, documented in 1663 by an Italian, Sebastiano Bado, was wrong on most counts and was disproved by the discovery in 1930 of the Viceroy’s official diary.

It turns out, for example, that Ana, the first Countess of Chinchon, died three years before Luis even went to Peru as viceroy. The second Countess of Chinchon, who did accompany Luis, was the picture of health the whole time but died on the journey from Peru back to Spain. But the (mis)story of Ana de Osorio persists to this day, like a virus that has become integrated into the DNA of our culture.

The Cinchona Tree

The bark of the Cinchona tree nonetheless bent the curve of medical and human history. It was brought by Jesuit priests to Europe, where the Spanish apparently knew of the bark’s medicinal value as early as the 1570s and was first used to treat malaria in Rome in 1631 (long before the mythical Ana even fell ill).

This bark, also called Jesuit’s bark or Peruvian bark at the time, became one of the most valuable exports from Peru when it became clear that it successfully treated malaria patients in Rome. Rome was once surrounded by marshes, and the name malaria comes from the medieval Italian words mala (bad) and aria (air). Malaria was associated with “bad air” emanating from Roman swamps.

Today we know that the cause of the disease is a single-celled parasite, Plasmodium falciparum, carried by mosquitoes that are endemic to marshlands.

Bad Air

Bad air was typically what Western medieval people blamed for any kind of disease. This was consistent with the ‘miasmic theory,’ passed down almost unchanged from ancient Greece a couple of millennia before. Microscopic organisms were not even known until Robert Hooke published his findings on them in 1665, followed soon after by Anton van Leeuwenhoek’s observations with his famous homemade microscopes. The role played by some of these microorganisms in human disease was still not recognized until Louis Pasteur’s experiments in the 1860s and Lister’s treatise on antisepsis which was published in 1867. Too late to mitigate the savagery of the American Civil War, which killed 2% of the population, most from disease (like malaria) and infection (doctors did not wash their hands or otherwise use aseptic technique while sawing off soldier’s mangled limbs).

But back to Rome, where malaria killed indiscriminately. Popes, cardinals, priests, and many other Romans — rich and poor — died miserably from the disease. The Jesuit’s knowledge of this bark’s curative abilities eventually led to its explosive rise in value and demand throughout 17th and 18th century Europe.

The Peruvian quinaquina tree eventually yielded a purified drug, the active ingredient called quinine, in 1820. Pierre Joseph Pelletier and Joseph Bienaime Caventou, French chemists who discovered caffeine and strychnine, among many other alkaloid plant compounds, found quinine was the active ingredient in the Peruvian tree bark.

Colonial Drugs

Quinine used as a drug enabled Europeans to colonize Africa. Native Africans had evolved certain traits associated with sickle-cell anemia and other genetic diseases, which gave them some resistance to malaria. Europeans did not have these genetic characteristics and were much more susceptible to the parasite. Africa became known as the White Man’s Grave. Quinine rectified that genetic deficiency and led to Europe rapidly colonizing and chopping up Africa in a global game of Risk.

The European’s colonial drive took them around the world, and quinine clearly enabled their global competition for territory, resources, and subjects, especially in equatorial and malaria-infested regions of the world. Although quinine is credited with saving many millions of lives over the centuries, one of the unintended consequences was that it enabled the Western powers’ colonial ambitions and conflicts, thus setting the stage for the slaughterhouse of World War I and its domino effect of WWII.

Quinine’s bitterness spurred British officials in various early 19th century colonial outposts to mix their medicine with soda and sugar — which marked the origin of tonic water. The British in colonial India mixed their tonic water with gin, creating a classic cocktail that is still embedded in our culture to this day.

The value of quinine rose rapidly, causing Jesuit’s bark to focus on global games of Risk and Monopoly. Peru and the neighboring countries tried to corner the market for their native Cinchona trees, but the Dutch managed to smuggle seeds out of South America. Eventually, Dutch plantations in Indonesia became the dominant world suppliers. The wily Dutch outplayed the South Americans and ended up with 97% of the global market and set up a quinine cartel in 1913 to control global supply and prices.

The 20th Century Drug

Quinine played a key role in one of the biggest successes and engineering marvels of the 20th century — the Panama Canal, built between 1904–1914 — driven by the big stick policies and willfulness of Teddy Roosevelt. There were many reasons for the failure of the early French efforts to build a canal across Central America. Still, the immense casualty rate among the engineering and labor forces certainly played a key role in France abandoning the project to the Americans.

Tropical diseases such as malaria were a major if not top contributor to French casualties. Central to the success of the American project was the groundbreaking public health initiatives driven by Dr. William Gorgas and his team — and their application of a new scientific understanding of malaria and other tropical diseases being transmitted by mosquitos. Mosquito control and prophylactic administration of quinine were among the cornerstones of their efforts.

Malaria also played an outsized role in the number of casualties during the First World War (disease — not the enemy — was usually the main killer of soldiers in wars throughout history). Before WWI, scientists and public health experts successfully controlled malaria in parts of Europe like Italy and Greece. However, these public health measures lapsed during the war, and also afterward: malaria became a global scourge again, well into the 20th century. Prophylactic use of quinine was studied and implemented by some countries during the Great War.

The late 19th and early 20th century were a sort of golden age of synthetic and organic chemistry, and quinine played a Muse’s role in this. Chemists tried to synthesize quinine since it was an expensive natural product (remember the Dutch cartel). Their efforts often failed miserably — but in a classic example of experimental serendipity — the failures sometimes bore fruit. William Perkin’s attempt in 1856 to make quinine resulted in abject failure and a mess, but the mess yielded a brilliant purple dye which made him a fortune. He was 18 years old.

The Age of Synthetics

Synthetic organic dyes, triggered by Perkin’s success, were one of the economic foundations of the German economy. Starting in the late 1860s, well-known companies formed that exists to this day: Bayer, BASF, Hoechst, etc.

A number of dyes were proposed as treatments for malaria, including methylene blue developed by Paul Ehrlich in 1890 and first used by him to treat malaria patients in 1891. Aside from not being as effective as naturally derived quinine, the dye-based malaria drugs had the unfortunate side effect of turning patients into various unnatural colors.

Finally, Hans Andersag, a researcher at Bayer AG in Germany, discovered a synthetic version of quinine in 1934 which eventually became known as chloroquine. Bayer ran clinical trials of these drugs in North Africa in the early 1940s during WWII, and this information fell into Allied hands around 1943. US doctors eventually recognized the efficacy of chloroquine, and it was approved for clinical use in the US in 1947.

During WWII, millions of US soldiers were given prophylactic antimalarial regimens, which resulted in a very unexpected and positive side effect. Clinicians noted reduced symptoms in those suffering inflammatory disorders such as skin rashes and some forms of arthritis after taking the drug. Clinical trials subsequently demonstrated the efficacy of antimalarials for a range of inflammatory diseases, starting with systemic lupus erythematosus in 1951. Today chloroquine analogs are administered off-label (i.e., not approved by the FDA) for a wide range of autoimmune diseases since they are among the few effective treatments that reduce symptoms. However, we still do not know exactly how chloroquine-based drugs blunt inflammation.

Another positive outcome of WWII was more organizational. The Office of Malaria Control in War Areas, established in 1942, was the immediate predecessor of the CDC, which was first known as the Communicable Disease Center when it kicked off on July 1, 1946. Malaria was the first target on its project roster, with the National Malaria Eradication Program starting a year after the CDC’s founding. Success was declared by 1951. Spraying DDT was one of the cornerstones of the CDC’s efforts to eradicate the mosquito vector of malaria, while chloroquine was the cornerstone of prophylaxis and treatment of the disease.

Where We Are Today

Hydroxychloroquine is a modification of chloroquine where a hydroxyl group (-OH) was appended to the side chain to reduce toxicity and was approved for medical use in the US in 1955.

In the years since chloroquine and hydroxychloroquine were approved in the US, we’ve learned a few things about these antimalarial drugs. We know now that these drugs accumulate in lysosomes and inhibit their acidification, which has subsequent effects on a range of cellular processes, including antigen presentation. We know these drugs reduce cytokine production by macrophages and inhibit toll-like receptor signaling and a variety of other immune pathways. But we remain far from causally linking the drugs to these disparate biological effects or ultimately to their clinical efficacy (against malaria or various inflammatory diseases).

Our long history of using these drugs has given us some insights into their limitations, side effects, and adverse drug interactions. One of the more severe side effects includes QT prolongation, an electrical disturbance of the heart that can lead to a fatal arrhythmia. Another is a 30% mortality among patients administered hydroxychloroquine who also took metformin, an important anti-diabetic drug.

In the US, malaria is no longer a significant clinical problem. But hydroxychloroquine and its analogs are prescribed for a wide range of debilitating autoimmune diseases, and many patients have come to rely on these drugs.

Then in 2020, dubious and poorly executed clinical studies hyped the effects of hydroxychloroquine and falsely claimed this drug had beneficial effects on COVID-19 patients. Didier Raoult, who masterminded these efforts, has since been censured and his papers retracted.

No placebo-controlled, double-blinded, sufficiently-powered clinical studies show hydroxychloroquine works against COVID-19.

Diabetics have a worse outcome with COVID-19, and these patients likely take metformin which is known to have lethal interactions with hydroxychloroquine.

In the rest of the world, over a million people per year, mostly pregnant women and young children, still die from malaria. But in a typical display of poorly allocated healthcare capital, we spend more on baldness treatments than for antimalarial treatments. Drug resistance has become a significant problem in many parts of the world so the need to invest in more antimalarial drug development is acute — but we still mostly use drugs that are almost a century old.

We’re gradually learning more and more molecular details of the intricate and complex life cycle of Plasmodium falciparum, the malaria parasite. Here are a couple of beautiful animations that show how malaria moves through the human host in one video and in the mosquito host in the other.

Molecule Allows Malaria Parasite to Commandeer Red Blood Cells
Two groups of HHMI scientists working independently have identified a critical enzyme that allows a malaria-causing…www.hhmi.org.

I don’t think there is anyone left who believes hydroxychloroquine works against COVID-19. If there are, if it is you, don’t be the last sucker buying snake oil. Instead, get vaccinated against COVID-19. Today.

The post The Evolution of Quinine to Hydroxychloroquine, Covid’s Snake Oil appeared first on Medika Life.

Many of us, as kids, memorized The Central Dogma of biology the way we memorized the scales. “DNA makes RNA makes protein” we recited as good students. “Do re me”. “Biological information flows along a one-way street” we’d chant to get extra credit or a gold star. 

Most of us are not surprised that music theory dives far deeper and spreads far wider, into alternate scales, chord progressions, counterpoint, and a plethora of foreign terms that would make any scientist proud.

Likewise, The Central Dogma has always been more nuanced than that three-step flow of biological information, DNA makes RNA makes protein. And it was always meant to be less dogmatic than the unfortunate name suggests.

A new paper, published a month ago in Science Advances, shows that human cells can make DNA from RNA, reversing the direction of information flow as we memorized it. But is it really reversed? What did The Central Dogma really say?

It’s a dogma eat dogma world…

The Central Dogma was first articulated by Francis Crick, half of the dynamic DNA duo, he and James Watson. Watson and Crick won the 1962 Nobel Prize in Physiology or Medicine for their discovery of the structure of DNA in 1953. This was a monumental breakthrough that established this immensely long molecule as the information carrier within all cells.

DNA carries instructions for making proteins, arguably the biological stuff that makes us who we are.

From 1956–1957 Francis Crick gave lectures about his speculations on gene function and how information flowed in biology. The following is the key page from his lecture notes:

Crick called his model The Central Dogma in typically bombastic style. However, when you read his notes above, it is clear that Crick was only articulating a hypothesis about gene function and information flow. In fact, he later acknowledged that he was mistaken and did not truly understand the meaning of dogma, and that it would have been better to call it a “basic assumption”.

The hand-drawn arrows show one set of paths that confirm what we memorized as kids, that “DNA makes RNA makes protein”. However, we see immediately that the Central Dogma is more complex than that simple do-re-mi version.

Crick assumed (since there were no experimental data to support his hypotheses at the time) that DNA could direct the synthesis of DNA (the circle arrow under DNA), that RNA could direct the synthesis of RNA (circle arrow under RNA), and that DNA could directly make protein without an RNA intermediate. Crick also, importantly, drew a dashed arrow going from RNA back (backwards!) to DNA.

The more important part of The Central Dogma is what it claimed cannot happen. We, in our abridged version, say that “information cannot go backwards”. That forwards is “DNA makes RNA makes protein”. But Crick specifically outlined the paths which cannot happen in his hypothesis. Protein cannot direct the synthesis of protein (the circle arrow under protein). And protein cannot direct the synthesis of RNA or DNA.

But note, in the “never” schematic, there is no arrow from RNA to DNA. That is allowed. 

And again, we have the dashed line in the “may be able to have” schematic that goes from RNA to DNA. The reverse of our cherished Central Dogma. Our erroneously memorized and abridged version.

The (Real) Central Dogma, the more complex one, has always considered the RNA to DNA path to be a reasonable possibility.

Filling in the dashed arrow…

It’s one thing to draw arrows. It’s much harder to figure out the nuts and bolts of what makes the arrow go — to find the mechanism that pushes a biological process forward. Just like we can easily draw an arrow from Boston to Chicago. But that arrow doesn’t tell us what mode of transportation we take, how the engine in that vehicle works, the arrangement of stator and rotors for DC or AC current, etc.

For example, let’s look at the circular arrow in Crick’s diagram under DNA. That means that DNA provides the information to make more DNA. How does that work in practice? Recall, none of this was known in 1956 when Crick first proposed this.

It turns out that there is a complex molecular machine, a protein, called a DNA polymerase. This enzyme reads DNA like a template and makes the matching strand of complementary DNA.

Recall that there are two strands of DNA, each strand is made up of a sugar-phosphate backbone, like a chain of identical repeating units, and like a flag, waving at each link of the chain is one of four bases which we abbreviate with the letters A, G, C, or T. Wherever there is an A in one strand of DNA, the complementary strand has a T that matches up with the A like a puzzle piece. Wherever there is a G, it is matched to a C. A base pair. 

The DNA polymerase does this by reading one strand of DNA, and where there is a base, a letter, it builds the second DNA strand with the complimentary base. A to T, and G to C, and vise versa for each. See the illustration below to see how the polymerase makes base pairs as it builds the new DNA strand from the template:

The first DNA polymerase was discovered in bacteria in 1956, about the time Crick was giving his Central Dogma lectures. Quite rapidly, scientists found bacteria had many different types of DNA polymerase, each doing different jobs. One polymerase started the process of copying DNA. Another polymerase finished copying. Yet another polymerase, several actually, repaired damaged DNA.

Our genome has over six billion base pairs, pairs of letters, in each cell in our body. The DNA polymerase must copy all six billion base pairs each time the cell divides since each daughter cell must get an identical copy.

That copying is essential to life, and errors in copying are at the root of many of our most troublesome diseases such as cancer. Therefore, DNA polymerases are among the most studied enzymes, or protein machines, in biology.

One of the things we’ve learned is that the human genome encodes for at least 14 DNA polymerases. 

One of the 14 is called polymerase θ (theta). This is an odd polymerase because it is very error-prone (it lacks the proof-reading ability that other polymerases have), and unlike most polymerases, it doesn’t require a template. When there is a template for polymerase θ, it is not particularly fussy about the quality or quantity of the template. Biologists give this unfussy enzyme a rather judgmental descriptor: promiscuous. Most enzymes (including polymerases) are very precise and picky about the molecule they pair with, unlike promiscuous enzymes such as polymerase θ.

The purpose for such an unusual enzyme as polymerase θ has puzzled biologists for decades. The main hypothesis was that this enzyme’s main job was to repair broken DNA or to help the cell tolerate such extreme damage.

Wrong way on a one-way street…

In 1970, more than a decade after Crick’s Central Dogma lectures, two biologists, David Baltimore and Howard Temin, published papers back-to-back in Nature announcing the discovery of virus enzymes that could go backward from RNA to make DNA.

Baltimore and Temin won the 1975 Nobel Prize in Physiology or Medicine for their discovery of the enzyme now called reverse transcriptase. (Note, we don’t treat Nobel-winners any differently, since they are human and make mistakes like we all do — see here.)

Since the discovery of reverse transcriptases, most thought only viruses had this ability to go the wrong way on a one-way street (most biologists, even, did not get the nuance in Crick’s less-dogmatic Central Dogma model which suggested the possibility).

Now it turns out that polymerase θ in humans has this ability to go the “wrong way” as well. This was shown in experiments in a recently published study where polymerase θ was given only RNA as a template, yet it quite happily went the wrong way and made DNA. Polymerase θ made similar amounts of DNA as a known virus (HIV) reverse transcriptase. 

Even more interesting was the fact that polymerase θ generated DNA at a higher speed when using RNA as a template than when using DNA. Furthermore, the DNA reverse transcribed by polymerase θ was more accurate from an RNA template than from DNA.

Digging even further into the nuts and bolts, this study found polymerase θ bound more tightly to RNA than DNA and this was seen in atomic-resolution structural images (obtained using x-ray crystallography).

Closing the loop on the function of polymerase θ, the researchers found that this unique human DNA polymerase helps DNA repair by using RNA as a template.

Something absolutely fascinating about this seemingly unique DNA polymerase θ is that it is very closely related to the first DNA polymerase discovered in bacteria by Arthur Kornberg in 1956, called polymerase I. When the proofreading function of polymerase I was disabled (to be like polymerase θ), polymerase I could also reverse transcribe. Like polymerase θ. Like virus reverse transcriptases.

The final dogma…

Replication, repair, and maintenance of DNA is a core function in biology. The enzymes responsible for this essential function, DNA polymerases, are so important that they were probably among the first enzymes evolved in the first bacterial cells, and have been conserved even after billions of years of evolution, and remain in the recognizable form today from bacteria to humans.

One of the most important functions is the repair of DNA damage. One way to repair certain kinds of DNA damage is to use RNA as a template. This is the job of polymerase θ. A polymerase that goes the wrong way on a (supposedly) one-way street.

The post Central Dogma has Lost its Dog appeared first on Medika Life.

A few weeks ago a former journalist Nicholas Wade penned a long conspiracy “theory” pointing fingers at the Wuhan Institute of Virology for a possible lab leak causing the COVID-19 pandemic.

Wade quoted the Nobel-prize-winning virologist Baltimore in his piece:

“When I first saw the furin cleavage site in the viral sequence, with its arginine codons, I said to my wife it was the smoking gun for the origin of the virus,” said David Baltimore, an eminent virologist and former president of CalTech. “These features make a powerful challenge to the idea of a natural origin for SARS2,” he said.

Let’s reholster that smoking gun…

Kristian Andersen is a Ph.D. virologist who early in 2020 wrote an important Nature Letters paper showing that the SARS-CoV-2 virus was most likely a naturally derived virus and not engineered in a lab. Andersen responded to Baltimore’s smoking gun comment with some very specific tweets firmly debunking the smoke from any guns:

The furin cleavage site (FCS) / polybasic cleavage site is present in SARS-CoV-2 at the S1/S2 junction of the spike protein where it mediates the cutting (by the host protease furin, among others) of the spike, which is required for infection of cells.

This introductory tweet basically says that the FCS is like a flag within the virus’ spike protein for a human protein scissors called a furin to come and cut the spike. Cutting the spike at the location makes it much easier for the virus to then get into our cells.

Andersen provided a detailed map of that flag, shown below:

Andersen continued his scientific tweetise by explaining how the virus’ flag was made and what it does:

The FCS was created by an out-of-frame insertion of “CTCCTCGGCGGG” creating the “(P)RRAR” amino acid sequence, which constitutes a suboptimal polybasic cleavage site that is important for expanding SARS-CoV-2 host range, it’s transmission and pathogenesis, etc.

There’s a lot in that short sentence to let’s unpack that a bit.

Out-of-frame insertion…

Andersen’s comment about an out-of-frame insertion means that the DNA code CTCCTCGGCGGG is not read in the normal in-frame triplets CTC-CTC-GGC-GGG. If we consult a codon table we see that those codons translate into an amino acid sequence: L-L-G-G (or leucine-leucine-glycine-glycine). However, this short sequence was inserted into the virus genome out-of-frame so it was actually read nCT-CCT-CGG-CGG-Gnn. The first and last triplets are part of an existing codon with the letters nnn. So the middle three codons translate to: x-P-R-R-x. We have only a part of the FCS Andersen mentioned which is (P)RRAR — so where does the rest come from?

This dozen letters of genetic code was inserted within a previously existing codon, not between codons the way a scientist would engineer an insertion.

The previous amino acid was a serine. The codons for serine include: TCT, TCC, TCA, and TCG.

Since the first out-of-frame codon is nCT, we know that the original codon was TCT. The insertion happened between the first T of the serine codon, and the last two CT.

If our out-of-frame insert happens within this serine codon, we end up with the following: TCT-CCT-CGG-CGG-GCT.

Now if we translate that, we end up with the following: S-P-R-R-A.

The original amino acid next to the serine is an arginine, R. Therefore the full sequence including the original S-R becomes: S-P-R-R-A-R.

Sub-optimal cleavage site…

Next, after explaining how the FCS was encoded by an out-of-frame insertion of a dozen nucleotides (genetic letters), Andersen then calls the result a “suboptimal polybasic cleavage site”. What does he mean by this?

A furin is a protein which is evolutionarily designed to cut other proteins. Enzymes like proteases, protein scissors that cut other proteins, typically recognize very specific targets. In our case, furins recognize short amino acid sequences and cut near those targets. The sequence furins recognize are: R-X-[K/R]-R↓. We know R = arginine, K = lysine, and X = any amino acid. The arrow designates where furin cuts the target protein.

The FCS in the SARS-CoV-2 virus is R-R-A-R and differs from that simple R-X-[K/R]-R motif. Furthermore, efficient cleavage requires more than four amino acids. Optimal furin cleavage sites actually requires about 20 amino acids. The following illustrates what is known as optimal furin cleavage sites:

For example, the viral sequence contains two isoleucines in the P3′ and P4′ region which calls for small hydrophillic amino acids, whereas isoleucines are aliphatic amino acids.

It is clear that the SARS-CoV-2 site works as a furin target, but is far from optimal.

Transmission and pathogenesis…

Finally, Andersen concludes his second tweet in this series by saying: “…polybasic cleavage site …is important for expanding SARS-CoV-2 host range, it’s transmission and pathogenesis…”.

Studies of coronaviruses without the furin cleavage site showed that this short insertion is essential for infection into human cells and is key to the transmission (ability to infect new hosts) and pathogenicity (ability to grow in the host cells) of this virus.

Importantly, the furin cleavage site may have been the key in the spread of this virus from the original bat host to humans, possibly through an intermediate species.

Where did FCS come from…

Andersen then beautifully addressed the question of where the FCS came from. I’ll just extensively quote from most of his thread here. He tweeted:

FCSs are abundant, including being highly prevalent in coronaviruses. While SARS-CoV-2 is the first example of a SARSr virus with an FCS, other betacoronaviruses (the genus for SARS-CoV-2) have FCSs, including MERS and HKU1.

He’s saying that evolution solved the “problem” of putting FCS into viral genomes many times. This is not unusual or difficult for viruses.

There is nothing mysterious about having a “first example” of a virus with an FCS. Viruses sampled to date only give us a teeny-tiny fraction of all the viruses circulating in the wild. Fragments — such as the CTCCTCGGCGGG — come and go all the time.

How did SARS-CoV-2 acquire the FCS? We don’t know, however, we know four main mechanisms often lead to insertions: (1) mutation (2) polymerase slippage (3) template switching (4) recombination All of which play key roles in coronavirus (incl. SARS-CoV-2) evolution.

While we don’t know for sure how SARS-CoV-2 acquired the FCS, template switching is a very likely explanation with a plausible mechanism: https://link.springer.com/article/10.1007%2Fs00705-020-04750-z … We also find insertions — albeit not FCSs (yet) — in highly related viruses, e.g., RmYN02:

Template switching likely also play an important role during the ongoing evolution of SARS-CoV-2: https://www.biorxiv.org/content/10.1101/2021.04.23.441209v1 …. We need to see this in the context of the decades of evolution of the SARS-CoV-2 ancestor and related viruses in bats. It’s safe to say indels come and go.

The FCS itself, (P)RRAR, is not an optimal site (for cleavage) and has never previously been used in CoV experiments to the best of my knowledge — unlike more optimal sites, which have been inserted into SARSr CoVs for basic research:

The exact same (P)RRAR FCS found in SARS-CoV-2 can be found in different viruses, including Feline coronavirus (FCoV), which is an alphacoronavirus. Note, site not present in all closely related viruses and plenty of indels around the site — like SARS-CoV-2 vs SARSr CoVs.

If we zoom in on the (P)RRAR site in SARS-CoV-2 and compare it to the one found in (some) FCoV sequences, we can see there’s a fair bit of homology outside the FCS too — including likely O-linked glycans being conserved.

The (P)RRAR FCS isn’t optimal and while it’s ‘sufficient’ for SARS-CoV-2s ‘success’ as a pandemic virus, it’s not an ideal site as defined by the canonical R‐X‐K/R‐R FCS seen in many proteins (viral and otherwise).

The “P” from the (P)RRAR insert isn’t directly part of the cleavage site itself, but, intriguingly, may regulate it via the nearby O-linked glycans. This is seen in host proteins: https://www.jbc.org/article/S0021-9258(20)32890-8/fulltext …, but also in SARS-CoV-2:

Importantly, however, in recent month we have started seeing the “P” mutating towards residues creating more optimal furin sites — P681H and, especially, P681R, which can be found in B.1.1.7 and B.1.617.x, suggesting the virus may evolve towards more efficient usage of the site.

So Baltimore’s first point — that the FCS found in SARS-CoV-2 is somehow unusual — is simply incorrect. FCSs are found in a multitude of different coronaviruses, indels come and go frequently, and the exact (P)RRAR can be found in other coronaviruses.

Now, the codons. Here, Baltimore is talking about the two codons coding for the first two arginines (R) following the P — CGG. The CGG codon is rare in viruses because it’s an example of an unmethylated “CpG” site that can be bound by TLR9, leading to immune cell activation.

Despite being rare, however, CGG codons *are* found in all coronaviruses, albeit at low frequency. Specifically, of all arginine codons, CGG is used at these frequencies in these viruses: SARS: 5% SARS2: 3% SARSr: 2% ccCoVs: 4% HKU9: 7% FCoV: 2% Nothing unusual here.

Furthermore, if we go back to the FCoV sequences and compare them to SARS-CoV-2 at the nucleotide level you’ll see that FCoV also uses CGG to code for R immediately following the P. The next R is CGA (non-CpG) in FCoV, while it’s CGG in SARS-CoV-2 — one nucleotide difference.

We see CGG multiple times in different ways — here’s an example comparing another “PR” stretch between SARS-CoV-2, RaTG13, and SARS-CoV in the N gene. Note how SARS-CoV-2 and RaTG13 both use CGG, while SARS-CoV-2 uses CGC for the first R, while later R’s are coded by CGT or AGA.

One final point about the CGG codons in the FCS — if they were somehow “unnatural”, we’d see SARS-CoV-2 evolve away from “CGG” during the ongoing pandemic. We have more than a million genomes to analyze, so what do we find if we look at synonymous mutations at the “CGG_CGG” site?

Remarkably stable. Specifically, CGG is 99.87% conserved in the first codon and 99.84% conserved in the second. This is *very* strong evidence that SARS-CoV-2 ‘prefers’ CGG in these positions.

R is coded by six different codons, yet the simple single transition “CGA” is only observed in ~0.02% of sequences. The second most ‘popular’ codon at these sites is “CGT” (a transversion) at 0.11% frequency. In other words — there is nothing unusual about the codons either.

So Baltimore’s second point is also false, invalidating his hypothesis that the “FCS […] with its arginine codons […] was the smoking gun for the origin of the virus”. Baltimore does not provide any evidence to support his hypothesis and the data support a natural origin.

Does this disprove a lab leak? No. However, it disproves there being a “smoking gun” in the FCS and lends further evidence to natural emergence — but it also does not *prove* that scenario. To this day, we have yet to see any scientific evidence supporting a lab leak.

Baltimore backs down…

In an interview with Nature and the Los Angeles Times, David Baltimore conceded that he went too far with his smoking gun comment. In an email to the LAT, Baltimore said that he

“should have softened the phrase ‘smoking gun’ because I don’t believe that it proves the origin of the furin cleavage site but it does sound that way. I believe that the question of whether the sequence was put in naturally or by molecular manipulation is very hard to determine but I wouldn’t rule out either origin.”

Where does that leave us…

Let’s get back to quoting Andersen who has been the most reliable and expert voice so far in all of these back-and-forth comments. Andersen emailed the LAT:

“We cannot prove that SARS-CoV-2 has a natural origin and we cannot prove that its emergence was not the result of a lab leak.

However, while both scenarios are possible, they are not equally likely,” Andersen wrote. “Precedence, data and other evidence strongly favor natural emergence as a highly likely scientific theory for the emergence of SARS-CoV-2, while the lab leak remains a speculative incomplete hypothesis with no credible evidence.”

The post Nobel-Winning Virologist David Baltimore Eats Wuhan Crow appeared first on Medika Life.

News organizations have latched onto Biden’s latest marching orders to the U.S. intelligence community to hustle up and, in the next 3 months, come to a conclusion on the origins of the COVID-19 pandemic:

“I have now asked the Intelligence Community to redouble their efforts to collect and analyze information that could bring us closer to a definitive conclusion, and to report back to me in 90 days. As part of that report, I have asked for areas of further inquiry that may be required, including specific questions for China. I have also asked that this effort include work by our National Labs and other agencies of our government to augment the Intelligence Community’s efforts. And I have asked the Intelligence Community to keep Congress fully apprised of its work.”

Biden said that in March he had asked his national security advisor Jake Sullivan to report on what is known about the origins of the SARS-CoV-2 virus at the heart of the pandemic.

The intelligence community has narrowed the field to two theories on the virus’s origin: a natural transfer from an animal host to humans or a laboratory accident. The majority of the community believes we lack “sufficient information to assess one to be more likely than the other.”

Of the 17 agencies within the intelligence community, two sided with the natural origins theory, and one with the lab release theory, but none with high confidence:

“…while two elements in the IC leans toward the former scenario and one leans more toward the latter — each with low or moderate confidence…”

So, what can we expect after Biden’s 90-day deadline?

WHO done it…

Back in January of this year, the World Health Organization sent an international team of virologists, epidemiologists, and other health scientists to Wuhan and surrounding areas to determine the origins of the virus. Half of the team were Chinese.

The team concluded that the most likely origin included an intermediate host, followed by direct transmission from the original host (called a spillover). Much less likely was a viral origin from food products, and that an origin from a laboratory accident was “extremely unlikely.”

Although the WHO report was very detailed, it was criticized in a couple of ways.

First, despite the comprehensive details in the WHO report, the study did not find or publish anything new. It contained all the known information about the virus and the COVID-19 disease put into one shiny package.

Second, despite pointing to an intermediate animal between the original bat host and the eventual human host, the WHO team did not find that hypothesized intermediate despite researchers testing “tens of thousands of wildlife and livestock samples.”

Third, the WHO team did not include anyone with a biosafety background to thoroughly investigate a possible laboratory origin. This led to the high-profile dissention of the WHO’s Director-General, Tedros Adhanom Ghebreyesus, who insisted on more work to investigate the lab leak hypothesis. Furthermore, 17 scientists signed a letter published in the journal Science calling for further investigation into the SARS-CoV-2 origins, including both lab leak and natural hypotheses.

The NYT reported that the scientists who signed the letter did not see a case for a lab leak:

Yet Dr. Iwasaki stressed that she did not see a clear case for a lab leak. “I’m completely open-minded about the possibilities,” she said. “There’s so little evidence for either of these things, that it’s almost like a tossup.”

For this to change significantly, we will need significant cooperation from the Chinese about what happened in key labs in Wuhan and ongoing investigations and sampling in various regions throughout China.

This ambiguous tossup between competing hypotheses will not likely change in 3 months.

Will China release any information…

No.

Biden’s 90-day prod to his intelligence agencies comes about partly from China’s refusal to take part in the second phase of the WHO’s investigation into the origins of COVID-19.

At the height of U.S. power and dominance in the global world order during and after World War II, no country in the world dictated terms to the U.S. This was especially true after the collapse of the Soviet Union in 1991. Even now, as the U.S. undergoes an inevitable and slow decline in power, no country in the world has ever sent inspectors into the U.S to inspect government facilities, companies, people, or animals, and in any way dictated terms to U.S. interests.

China is currently the #2 world power just behind the U.S. by many metrics such as GDP (and even exceeds the U.S. depending on the measures). The U.S. and China as economic peers are far ahead of the #3 economic power (either Japan or India depending on the measure).

Yet China is still considered by many as a developing country and is often treated as such. And by some measures such as per capita income or wealth, China is indeed ranked far below the U.S.

China is clearly insulted by demands that foreign investigators have unfettered access to Chinese labs, people, and countryside to interview, sample, and test at will to determine the cause the pandemic. Many around the world blame China.

To get a sense of China’s feeling of outrage and inequity, read this comment by Chinese foreign ministry spokesman Zhao Lijian:

“If the US side really wants a completely transparent investigation, they should invite the WHO experts to launch an investigation in the US.”

China’s intransigence is also not likely to change in 3 months.

Will we find out what happened in the Wuhan Institute of Virology…

No.

The Chinese will not suddenly see cooperating with the U.S. and the rest of the world as beneficial.

The Chinese government has a long-standing policy of secrecy and is almost genetically programmed to obstruct open and cooperative global projects, especially on its soil.

Also, the US demonstrated the petulant, xenophobic, and racist instincts of a virulent American minority by their treatment of China from 2016 to 2020, and especially during the pandemic. That is now bearing fruit in China’s complete refusal to cooperate.

China is digging in its heels and being equally petulant, denying the lab leak hypothesis while also failing to gain confidence with the global community. Chinese foreign ministry spokesman Zhao Lijian said:

“Some people in the United States completely ignore facts and science.”

Zhao’s comment was true for the Trump administration, but clearly not for Biden’s. But just as important, China is not providing the facts and science that would help exonerate them or help understand their role in the pandemic.

Nonetheless, Biden has kept pressure on the Chinese from the beginning to be open and transparent about the origins of the SARS virus and any information they have.

That will not happen, and our blindness to the happenings within the Wuhan Institute of Virology won’t change in 3 months.

Will the virus tell us anything about its origins…

Maybe.

All the biological information, specifically the genomic information contained in the RNA within the virus, is most consistent with a natural origin.

First, the genetic code itself, the proteins, and all the features of the proteins are consistent with a naturally evolved virus. In other words, evolution easily and parsimoniously explains every feature of the virus. No need to invoke little green men or wicked scientists in the making of the virus.

Second, there are no proteins, segments of proteins, or features of the genetic code that even hint at an artificial origin. For example, some COVID conspiracy theories point to the polybasic or furin cleavage site and the sequence coding as possible human tampering signs. That is incorrect. There are no hidden messages in the viral genome other than biological secrets.

Third, the basic genetics of the virus and its nearest viral cousins make it very unlikely to have been the product of an engineered human virus. Let’s dig into this last point because it is a little subtle.

The closest known virus to SARS-CoV-2 is the bat virus known as RaTG13. These two viruses are 96.2% identical across their whole genomes. However, the bat RaTG13’s spike or S protein binds poorly to human ACE2, while SARS-CoV-2 binds very well, explaining the latter’s effectiveness as a human pathogen.

Someone interested in engineering a highly effective human virus would have started with a known human pathogen such as the original SARS, now known as SARS-CoV or SARS-CoV-1. The RaTG13 virus, SARS-CoV-2’s closest cousin, would not have shown up on anyone’s radar as a promising virus to make into a human pathogen.

A pangolin coronavirus (Pangolin-CoV) contains a spike or S protein which is more closely related to SARS-CoV-2 than to RaTG13. Within the S protein, 5 amino acids are critical to effective binding to human ACE2 protein. Pangolin-CoV’s S protein keeps those 5 critical amino acids in common with SARS-CoV-2 and has only one non-critical amino acid that is different. RaTG13, on the other hand, has an S protein which is very different from SARS-CoV-2, with 17 amino acid differences, including 4 out of the 5 amino acids critical for ACE2 binding.

The chart below illustrates the similarities and differences in the spike protein amino acid sequences among almost two dozen viruses. Each letter represents an amino acid, with the full sequence of the SARS-CoV-2 virus along the top line. Each additional virus listed along the left side has a sequence compared to SARS-CoV-2 (called Beta-CoV/Wuhan-Hu-1). If the additional virus’s amino acid is identical to SARS-CoV-2, that is indicated with a dot. If the amino acid is different, the different amino acid’s abbreviation letter is shown.

This is one of the reasons that the pangolin was at one point thought to be the intermediate host between bat and human.

However, as Kristian Andersen points out in his important paper about the origins of COVID-19, the interaction of SARS-CoV-2 with ACE2 is not ideal. Therefore Pangolin-CoV’s S protein, though it happens to bind well to ACE2, is not predicted to be a good binding protein for the human receptor.

No scientist would have picked RatG13 as a base virus and substituted Pangolin-CoV’s S protein and thought that would be a good place to start developing a highly infectious human virus.

Sure, someone could conceivably have taken the RaTG13 bat virus with no ability to infect humans, and substituted a pangolin-CoV’s S protein, and made SARS-CoV-2. But no scientist would have picked those two viruses to merge in just that way as a promising track to create something worth their efforts.

Biology is crazy complicated. The genetic code is not as simple as four letters would have you believe. Many look at the letters of the genetic code and come up with imaginary patterns convinced of alien abduction, or virus-laden comets infecting an early Earth, or that a polybasic cleavage site with human codons was inserted into a benign virus to make a human super-virus.

There is an endless line of people submitting papers claiming to debunk Einstein, or claiming to have built a perpetual motion machine or cold fusion reactor, or having proven that China built and released the SARS virus. They are not stupid people standing in that imaginary line. They are generally educated, just enough to be dangerous. And they are very wrong.

None of these things will change considerably in the next 3 months.

High-tech spooks…

The NYT speculated that the Biden push will activate the intelligence community to use “an extraordinary amount of computer power to the question of whether the virus accidentally leaked from a Chinese laboratory.” According to the Times article, the computing power may be used on a database of unanalyzed “Chinese communications, the movement of lab workers and the pattern of the disease outbreak around the city of Wuhan.”

However, the NYT cautioned that even this amped up silicon-assisted inquiry by the intelligence community is unlikely to turn up anything:

“Current and former intelligence officials say they strongly doubt anyone will find an email or a text message or a document that shows evidence of a lab accident.”

An excellent example of the limits of this intelligence work, even with international cooperation, is infection intelligence that the WSJ made a big splash about earlier in the week. The NYT said:

“One allied nation passed on information that three workers in the Wuhan virological laboratory were hospitalized with serious flulike symptoms in the autumn of 2019. The information about the sickened workers is considered important, but officials cautioned that it did not constitute evidence that they caught the virus at the laboratory — they may have brought it there.”

Again, it is unlikely that a few additional months of high-tech spookery will rustle up conclusive evidence that eluded previous work.

Right back where we are…

In conclusion, the probability is that 90 days from Biden’s statement, we will be back where we are now. That means the biological data is completely consistent with natural origins. The data needed to more confidently rule out a laboratory origin and require Chinese cooperation will be missing. That is because the Chinese will not cooperate and will effectively nullify any international efforts to penetrate their sources of information.

Thank you for reading and please doshare! Also, if you liked this, you might like the following:

Debunking Nicholas Wade’s Origin of COVID Conspiracy Theory

The post Predictions For Biden’s Covid Origin China Probe appeared first on Medika Life.

Nicholas Wade is wrong

The Wall Street Journal, meanwhile, has been busy pushing an “undisclosed U.S. intelligence report” suggesting that three Chinese researchers at the now-famous Wuhan Institute of Virology were hospitalized in November 2019. These workers had “symptoms consistent with both Covid-19 and common seasonal illness”.

Conspiracy theories of the COVID-19 virus SARS-CoV-2 originating in an accidental lab release being peddled by Trump’s former FDA commissioner and the WSJ are not surprising. Supporters of Trump clearly have no love of truth as witnessed by how the GOP is treating long-time uber-conservative party leader Liz Cheney.

The most recent salvo of dubious theories comes from Nicholas Wade, a former science writer for Nature and Science and the New York Times. Despite Wade’s journalistic pedigree, close reading of his latest essay on the origins of COVID-19 reveals a poor adherence to reporting standards, investigatory lapses and major biases, and insistent mis-representation or outright falsehoods, leading to erroneous and unsupportable conclusions.

Unfortunately, Wade’s conspiracy theory has already gotten significant press, and is notable mostly for his highly personal attacks on those with divergent views: Drs. Anthony Fauci and Francis Collins and Kristian Anderson and Peter Daszak are among his most prominent targets.

Wade promises to guide you through the molecular biology of viruses, but his promise is shallow. Wade’s essay shows that his biology knowledge is ankle-deep and packed with major and minor errors and misrepresentations. He has a bachelor’s degree in biology so he is not completely uneducated.

However, Wade proves the classic trope that a little knowledge is a dangerous thing. His essay is exactly that — a dangerous thing.

Let’s see why.

More personal than molecular biology…

Wade spends much of his essay doling out personal takedowns of some key coronavirus researchers who have communicated scientific observations contrary to his opinions. The first of many victims is Dr. Peter Daszak, and the second is Dr. Kristian Anderson, followed by others.

Let’s focus on Wade’s attacks on Dr. Anderson since Wade presses several buttons here. First, Dr. Anderson and his team published a Nature letters article early during the pandemic explaining why an engineered origin of the virus was unlikely.

In the first step of Wade’s assault, he characterizes Anderson’s Nature letter as “…an opinion piece, not a scientific article…”. Wade’s Wikipedia page says that he was an editor at prestigious scientific journals Nature and Science, and therefore clearly knows better. Wade’s claim that a Nature letter like Anderson’s is only opinion and not a scientific article is not a small error, but an intentional assault on facts and truth.

A blog by Nature lays out the difference between these two formats quite clearly:

Articles are original reports whose conclusions represent a substantial advance in understanding of an important problem and have immediate, far-reaching implications.

Letters are short reports of original research focused on an outstanding finding whose importance means that it will be of interest to scientists in other fields.

Nature letters are NOT merely opinions. This has been a long-standing feature of Nature. As a prime example, the biggest biological discovery in the 20th century may be Watson and Crick’s discovery of the double-helical and complementary nature of DNA’s structure — published in a Nature letter. Clearly not just an opinion piece.

Any science writer knows that a couple of the most important science journals are called Physics Letters A and Physics Letters B.

These Nature letters represent important scientific reports. Clearly Wade found it necessary to jettison his editorial knowledge from working at that very journal in order to diminish and dismiss Anderson’s data, discussions, and conclusions.

Furthermore, when Wade tries to tackle Anderson’s data, he remains firmly in personal attack mode with comments like:

…Unfortunately this [Anderson’s article] was another case of poor science…

Wade liberally sprinkles much more of these snide and passive aggressive attacks throughout his essay. A journalist passing judgement on a scientist’s science, suggesting himself as more knowledgeable than the scientist, and co-opting a position as a science educator while peddling obvious errors and alternative facts as science.

A poor attempt at molecular biology…

When Wade finally argued Anderson’s data and discussions, we immediately saw how out of his depth and off target he was — and therefore why he spent so much time trying to damage those with opposing views. Wade clearly found that damaging reputations was much easier than arguing the points of a field in which he was unqualified.

The first argument Wade made with Anderson was about seamless methods of cloning or DNA manipulation. Wade referred to early methods of molecular cloning that left easily detected remnants or scars in the DNA sequence. The trouble with this is that Anderson never invoked genomic scars in his paper.

Perhaps Wade was familiar with seamless cloning technology — if your only tool is a hammer, everything is a nail. One such technology was called “No see’m” and was developed and used by coronavirus researchers. Aside from Wade’s error in calling it “No-see-um” which is a type of incredibly irritating biting gnat, his bigger error is that his argument was irrelevant.

Anderson’s article said nothing about seamless technology, and instead said the following:

…Furthermore, if genetic manipulation had been performed, one of the several reverse-genetic systems available for betacoronaviruses would probably have been used19. However, the genetic data irrefutably show that SARS-CoV-2 is not derived from any previously used virus backbone20.…

Anderson was referring to a characteristic set of restriction sites, natural or engineered, necessary to work with each of the reverse genetic systems — nothing to do with seamless cloning.

Reverse genetics covers a broad range of scientific methods, but common among all is the idea of changing the DNA sequence (what biologists call the genotype) and then looking for changes in the organism (its features, behaviors, chemistry, etc., all lumped under a typically obtuse scientific term, phenotype). When applied to viruses, often the goal is to see when a non-human virus becomes capable of infecting human cells.

Then Wade tried to falsely characterize one of Anderson’s arguments:

…they [Anderson et al] say that the spike protein of SARS2 binds very well to its target, the human ACE2 receptor, but does so in a different way from that which physical calculations suggest would be the best fit. Therefore the virus must have arisen by natural selection, not manipulation…

This is a major misrepresentation and oversimplification of Anderson’s argument. The S protein shows strong binding affinity for the human ACE2 protein, but ALSO to ACE2 proteins from other species. The viral S protein evolved in a way that bound well, but not optimally to human ACE2. Any synthetic S protein would have been engineered specific to human ACE2, and the binding would have been much more “tailored”.

What Anderson actually said was:

…SARS-CoV-2 …binds with high affinity to ACE2 from humans, ferrets, cats and other species with high receptor homology… SARS-CoV-2 may bind human ACE2 with high affinity, computational analyses predict that the interaction is not ideal7 and that the RBD sequence is different from those shown in SARS-CoV to be optimal for receptor binding7,11. Thus, the high-affinity binding of the SARS-CoV-2 spike protein to human ACE2 is most likely the result of natural selection on a human or human-like ACE2 that permits another optimal binding solution to arise. This is strong evidence that SARS-CoV-2 is not the product of purposeful manipulation…

What Anderson meant was that computational calculations show that the binding between the viral S (spike) protein and the human ACE2 protein are not “ideal” — ideal being what we expect from an engineered S protein. An engineered SARS virus might have used one of two routes:

• Insert into the viral genome a known S protein with strong binding to human ACE2 protein.
• Passage through cells and use only human ACE2 as the target.

Either route would have resulted in a much better, more customized fit of S protein to human ACE2.

Anderson argued that there were multiple ACE2 protein targets including those from human and other animals, which strongly suggests a natural origin.

The fact that Wade did not understand this basic biological concept shows how lacking his technical background is, and emphasizes his lack of qualification to pass judgement on the scientists or science being discussed.

The irony is that Wade tried hard to imply that it was Anderson, the Ph.D. virologist, who lacked technical understanding of virology. Wade says of Anderson:

…The authors’ basic assumption, not spelt out, is that anyone trying to make a bat virus bind to human cells could do so in only one way. First they would calculate the strongest possible fit between the human ACE2 receptor and the spike protein with which the virus latches onto it. They would then design the spike protein accordingly (by selecting the right string of amino acid units that compose it). But since the SARS2 spike protein is not of this calculated best design, the Andersen paper says, therefore it can’t have been manipulated…

Note how Wade tries to tell us what Anderson’s assumption is? He tells us that the “authors’ basic assumption, not spelt out, is that anyone trying to make a bat virus bind to human cells could do so in only one way.” That is emphatically NOT Anderson’s basic assumption.

Anderson et al are virologists and they know (far better than Wade) how scientists design viral proteins. Wade packed false assumptions into Anderson’s head and article, concepts which are clearly wrong.

Wade worked hard to tell us that a Nature-published virologist made incorrect assumptions about how virologists design and make viral proteins — and then wants to tell us how virologists really do this work?

Read what Wade goes on to say:

…But this ignores the way that virologists do in fact get spike proteins to bind to chosen targets, which is not by calculation but by splicing in spike protein genes from other viruses or by serial passage…

Anderson’s comment on computation had nothing to do with engineering the virus — Wade mischaracterized and twisted Anderson’s intent. Anderson only discussed the after-the-fact computation of protein binding.

By the way, Wade also erred by saying that virologists don’t use calculations to design protein binding. Here is only one example of many articles showing how virologists DO indeed use computation to design protein-protein binding interactions.

Wade was wrong TWICE in one argument — Wade was wrong because virologists do indeed use calculations and computation to design protein-binding interactions — and Wade was also wrong because Anderson’s article never discussed that kind of computation.

Wade then tried to argue further:

…the Andersen group writes, and since SARS2 is not derived from any of them, therefore it was not manipulated. But the argument is conspicuously inconclusive. DNA backbones are quite easy to make, so it’s obviously possible that SARS2 was manipulated using an unpublished DNA backbone…

Wade clearly doesn’t understand the field and assumes that any DNA backbone will work. That is not true and is why the few backbones developed took so long, and are still used. They work.

Development of mouse hepatitis virus and SARS-CoV infectious cDNA constructs – PubMed: The genomes of transmissible gastroenteritis virus (TGEV) and mouse hepatitis virus (MHV) have been generated with a…pubmed.ncbi.nlm.nih.gov

Here are some comments from a real virologist that directly refute what Wade says is “quite easy to make”:

… To reiterate, most of SARS-CoV-2 comes from a bat coronavirus closely related to RaTG13. This virus is not known to cause disease in humans. If we were virus engineers (and this actually happens to be my job in the Benhur Lee Lab) we would need to:

Make a virus backbone from a never-before-seen virus that looks like, but isn’t, RaTG13 without having any reason to believe it would be a better starting place than a previously characterized virus (like the original SARS-CoV)

Spend months to years building a system that is easy to engineer (reverse-genetics system) when there are other virus backbones readily available.

Choose the RBD region from an unknown pangolin coronavirus even though all computer models show it should be suboptimal at binding ACE2, and show that it binds well in spite of the models (paper 1, paper 2, paper 3, paper 4)

All of these steps sound like bad ideas from a scientist’s perspective: there were easier ways to engineer a coronavirus, and no one would have rationally chosen either the bat virus backbone or the pangolin portion of the spike protein. Therefore, SARS-CoV-2 is unlikely to be man-made from pieces of other viruses — we have zero evidence that any person or lab has attempted even one part of this process.…

Then Wade minimized Anderson’s paper as follows:

…And that’s it. These are the two arguments made by the Andersen group in support of their declaration that the SARS2 virus was clearly not manipulated. And this conclusion, grounded in nothing but two inconclusive speculations, convinced the world’s press that SARS2 could not have escaped from a lab. A technical critique of the Andersen letter takes it down in harsher words…

Wade clearly didn’t understand that Anderson discussed several other important points including something called a polybasic cleavage site. This is a short sequence of amino acids which is a target for protein scissors called proteases. Proteases clip proteins at specific cleavage sites defined by a short amino acid sequence. Anderson et al discuss how a cleavage site can be acquired by the influenza hemagglutinin protein by repeated passage in cell culture or animals. Anderson also talks about its absence in most viruses closest to SARS2, that the RaTG13 is 96% identical but differs significantly in the RBD, but the pangolin CoV are similar to SARS2 especially the 6 key resides in the RBD. Anderson also says:

…a hypothetical generation of SARS-CoV-2 by cell culture or animal passage would have required prior isolation of a progenitor virus with very high genetic similarity, which has not been described. Subsequent generation of a polybasic cleavage site would have then required repeated passage in cell culture or animals with ACE2 receptors similar to those of humans, but such work has also not previously been described. Finally, the generation of the predicted O-linked glycans is also unlikely to have occurred due to cell-culture passage, as such features suggest the involvement of an immune system18…

Now that we are aware of how shallow Wade’s understanding of biology is, it is no surprise that he completely missed the point about O-linked glycans, and that they only form when the virus is exposed to an immune system.O-linked glycans on viruses are thought to shield them from their host’s immune system. Therefore, the presence of these sugars (and the amino acids which host them), strongly point to the virus’s evolution in an adaptive immune system such as ours.

Trying to cast doubts on natural emergence of SARS-CoV-2…

Wade next tried to cast doubts on natural emergence of SARS-CoV-2. He pointed to the WHO’s visit to China and that “the Chinese had no evidence to offer the commission in support of the natural emergence theory”. What Wade failed to mention is that the US harangued China during the Trump administration, and the Chinese probably and understandably felt no inclination to openly share data with the US or the rest of the world. We would do the same even though that is not responsible or the right thing to do. But most of us are unlikely to do the responsible and right thing when we have just been admonished and insulted on the world stage.

We clearly need China to be a good global citizen and to be open and honest about what they have found, to share their data as well as processes and procedures within their research institutes that may have in any way contributed to the pandemic (or not). In order for China to act like a good global citizen, we need to treat them as such, the way we would want to be treated.

Lacking China’s data, we are missing valuable information needed to refute or prove the lab escape thesis. We don’t know what we don’t know. Nonetheless, the existing biological data rests strongly on the side of natural emergence.

Wade claimed that the lack of evidence from China supports a lab-release of SARS-CoV-2 and against natural emergence. When in fact it merely emphasizes the Chinese government’s troublesome policy of secrecy.

Wade says, “… Natural emergence remained a conjecture which, however plausible to begin with, had gained not a shred of supporting evidence in over a year”. In fact, the evidence more powerfully supports natural emergence as Anderson’s Nature paper indicated.

Wade further showed his confusion about science by making it seem fast and easy to track down viral hosts and the evolution of previous coronavirus pandemics, saying:

…This was surprising because both the SARS1 and MERS viruses had left copious traces in the environment. The intermediary host species of SARS1 was identified within four months of the epidemic’s outbreak, and the host of MERS within nine months. Yet some 15 months after the SARS2 pandemic began, and a presumably intensive search, Chinese researchers had failed to find either the original bat population, or the intermediate species to which SARS2 might have jumped, or any serological evidence that any Chinese population, including that of Wuhan, had ever been exposed to the virus prior to December 2019…

When in fact, tracing down these viruses is a huge amount of work and actually took over a decade, not months. The finds virologists made for SARS1 and MERS were a combination of massive epidemiological efforts and huge luck.

It took 15 years after SARS1 to identify the animal origin of that pandemic. Finding the civet intermediary for SARS1 was a lucky strike which was not replicated for the original source of the virus.

Wade repeatedly pushed this idea that we should have found evidence already:

…Natural emergence remained a conjecture which, however plausible to begin with, had gained not a shred of supporting evidence in over a year…

And we see why he is so anxious for this exploration to have yielded conclusive results, because he says:

…as long as that remains the case, it’s logical to pay serious attention to the alternative conjecture, that SARS2 escaped from a lab…

The logic is quite the reverse. The evolutionary pedigree of the virus is an important part but only part of the tapestry of data which builds the case for natural emergence. The lack of host species is merely that — a lack that will eventually be filled in. The lack of this data does not automatically make lab escape a more plausible hypothesis. The genomic and genetic data that Anderson and others have established continue to be best explained by natural emergence.

The pot calling the Chinese kettle black…

Wade also tried to set the stage of the Chinese virus research and show how terrible their efforts were. He quoted from two research grants:

RePORTER: Grant Link

Federal RePORTER: Grant Link

Wade then selectively quoted two technical aims of the proposal and then interpreted them in a way to give them a most sinister mad scientist purpose:

… What this means, in non-technical language, is that Dr. Shi set out to create novel coronaviruses with the highest possible infectivity for human cells. …

No. That is not the correct way to interpret those aims. First, let’s provide the overall goal of this project to establish context — always an important journalistic principle:

…This project seeks to understand what factors allow animal Coronaviruses to evolve and jump into the human population by studying virus diversity in a critical group of animals (bats), a sites of high risk for emergence (wildlife markets) in an emerging disease hotspot (China)…

And one of the specific aims to meet that goal was to:

… to test the hypothesis that % divergence thresholds in S protein sequences predict spillover potential…

Threshold is the key term. You cannot make a predictive model of infection by creating something that has, as Wade says, “the highest possible infectivity for human cells”.

Instead, the goal is to sneak up on the smallest amount of genetic change, the threshold, at which a non-human virus becomes a human virus. Making the virus maximally infective tells you nothing other than it makes people sick, that it can infect humans.

Scientists are more subtle than what Wade communicated or understood. Finding the threshold, or minimum genetic change to trigger human infections, gives scientists tremendous predictive power. Finding a maximally infective virus does nothing other than bestow dubious bragging rights.

Again, when Wade offered to explain to you the reader what the technical meaning of something in a scientific document, I hope you have learned not to trust his claim or promise.

Wade also spent considerable effort discussing laboratory safety levels such as here:

… There are four degrees of safety, designated BSL1 to BSL4, with BSL4 being the most restrictive and designed for deadly pathogens like the Ebola virus.…

And then he made sure to take a quote out of context, trying to maximize the impression that the Chinese work was substandard by saying:

…Much of Dr. Shi’s work on gain-of-function in coronaviruses was performed at the BSL2 safety level, as is stated in her publications and other documents. She has said in an interview with Science magazine that “The coronavirus research in our laboratory is conducted in BSL-2 or BSL-3 laboratories.” …

Although Wade provided the link to the Science interview, he knows that most people do not take the effort to click the link and read. It is worth your time if you have read that far in his (and my) article.

Again, let’s provide a little context. The question by Science Magazine was as follows:

…Given that coronavirus research in most places is done in BSL-2 or BSL-3 labs — and indeed, you WIV didn’t even have an operational BSL-4 until recently — why would you do any coronavirus experiments under BSL-4 conditions? …

Notice that? Most places do coronavirus research in BSL-2 or BSL-3 labs, so there is nothing unusual in Chinese labs doing the same.

Dr. Shi’s response was:

… The coronavirus research in our laboratory is conducted in BSL-2 or BSL-3 laboratories.

After the BSL-4 laboratory in our institute has been put into operation, in accordance with the management regulations of BSL-4 laboratory, we have trained the scientific researchers in the BSL-4 laboratory using the low- pathogenic coronaviruses as model viruses, which aims to prepare for conducting the experimental activities of highly pathogenic microorganisms.

After the COVID-19 outbreak, our country has stipulated that the cultivation and the animal infection experiments of SARS-CoV-2 should be carried out in BSL-3 laboratory or above. Since the BSL-3 laboratories in our institute do not have the hardware conditions to conduct experiments on non- human primates, and in order to carry out the mentioned research, our institute had applied to the governmental authorities and obtained the qualification to conduct experiments on SARS-CoV-2 for Wuhan P4 laboratory, in which the rhesus monkey animal model, etc. have been carried out.

The experimental activities are supervised by our institute’s biosafety committee and complied with the biosafety regulations.…

Going batty…

Wade then tried to teach us about bat biology:

…The two closest known relatives of the SARS2 virus were collected from bats living in caves in Yunnan, a province of southern China. If the SARS2 virus had first infected people living around the Yunnan caves, that would strongly support the idea that the virus had spilled over to people naturally. But this isn’t what happened. The pandemic broke out 1,500 kilometers away, in Wuhan…

Spillover of the virus from bats to people directly is only one possible way SARS-CoV-2 evolved. However, even if that happened, spillover probably did not happen near the first discovery site of the virus. We should ask what is the range of the carrier (NOT to put a pin in a map where the virus was first discovered and limit our assumptions about where spillover happened).

Wade then continued:

…Beta-coronaviruses, the family of bat viruses to which SARS2 belongs, infect the horseshoe bat Rhinolophus affinis, which ranges across southern China. The bats’ range is 50 kilometers, so it’s unlikely that any made it to Wuhan. In any case, the first cases of the Covid-19 pandemic probably occurred in September, when temperatures in Hubei province are already cold enough to send bats into hibernation…

An individual animal’s range is not a hard limit like a car’s. Animals often far exceed the normal range, so a journalist claiming “so it’s unlikely” is far from the reality. Furthermore, hibernation is not a period of complete inactivity in bats. Bats show significant activity during hibernation even in the depths of winter when torpor is highest. September in Hubei, the temperature ranges from 4–15C, so hibernation is neither required nor absolute during such a mild month.

Wade then tries to make the chain of virus infections seem like an exercise in improbabilities by saying certain conditions “must” occur on his say-so:

…What if the bat viruses infected some intermediate host first? You would need a longstanding population of bats in frequent proximity with an intermediate host, which in turn must often cross paths with people. All these exchanges of virus must take place somewhere outside Wuhan, a busy metropolis which so far as is known is not a natural habitat of Rhinolophusbat colonies. The infected person (or animal) carrying this highly transmissible virus must have traveled to Wuhan without infecting anyone else. No one in his or her family got sick. If the person jumped on a train to Wuhan, no fellow passengers fell ill…

Wade concocted a story of false improbabilities — he arbitrarily states conditions: “What if the bat viruses infected some intermediate host first? You would need a longstanding population of bats in frequent proximity with an intermediate host…”. No. Are there well-established conditions for spillover of virus from bats into other species? Where does Wade get the condition that a longstanding population of bats must be in frequent proximity with the host? Is that a known requirement? Says who? Must there be frequent proximity? Must the infected intermediate host often cross paths with humans? Who says? Wade?

Why MUST these virus exchanges in an intermediate host be outside Wuhan? The first SARS began in a city — Foshan in Guangdong province, originated in bats, and through a civet intermediate before spreading in humans with high mortality (10%).

It took 15 years after SARS1 to identify the animal origin of that pandemic. The lack of clear evidence of a natural origin for SARS2 is NOT a strike against that hypothesis — lack of data is only that — a lack of data.

The SARS1 pandemic was in 2002–3, and Shi was unable to identify the bats from which it originated, and passed through civets to humans, until 2013. And it wasn’t until 2017 that scientists identified the single population of bats from which the first SARS virus originated.

So, pointing to the knowledge of SARS1 now, and the lack of similar knowledge for SARS2 is highly deceptive and misleading.

Furin cleavage site…

Wade continues his assault on facts and biology on an important part of the SARS-CoV-2’s spike protein:

…The furin cleavage site is a minute part of the virus’s anatomy but one that exerts great influence on its infectivity. It sits in the middle of the SARS2 spike protein. It also lies at the heart of the puzzle of where the virus came from… of all known SARS-related beta-coronaviruses, only SARS2 possesses a furin cleavage site. All the other viruses have their S2 unit cleaved at a different site and by a different mechanism…

Wade purposely exaggerates the rareness of SARS-CoV-2 possessing a furin cleavage site. There are only four SARS-related betacoronaviruses — SARS-CoV-1 and -2, RaTG13, ad SL-CoV-WIV1. And indeed SARS-CoV-2 is the only betacoronavirus with a furin cleavage site. ONLY one of four!

What Wade conveniently neglects is that Furin cleavage sites are common in coronaviruses, and is present in a virus which is evolutionarily close to SARS-CoV-1 and -2. A Hibecovirus, close relative to the sarbecovirus (the family to which SARS-CoV-1 and -2 belong) and which infects the Hipposideros bat, has a furin cleavage site at the same location in the S protein. Wade is not correct to wave away the lack of furin cleavage sites in this virus family.

Again, Wade fails in his promise to teach you some molecular biology of viruses when he claims:

…How then did SARS2 acquire its furin cleavage site? …Two ways viruses evolve are by mutation and by recombination… Beta-coronaviruses will only combine with other beta-coronaviruses but can acquire, by recombination, almost any genetic element present in the collective genomic pool. What they cannot acquire is an element the pool does not possess. And no known SARS-related beta-coronavirus, the class to which SARS2 belongs, possesses a furin cleavage site…

There are more than two ways for RNA viruses to obtain mutations. A very important mechanism which Wade is ignorant of is something called copy-choice recombination or template switching, where the RNA-dependent RNA-polymerase changes template in the middle of making copies of the viral RNA.

More broadly, template switching allows RNA viruses to recombine with unrelated viruses:

Wade insists that this acquisition of a furin cleavage site is a rare or impossible event, and it is not.

Wade further confuses the molecular biology of viruses by claiming that human codons, the three-letter code which translates the genetic code into amino acids, were used in the furin cleavage site, and that is highly suscpicious evidence of human interference in virus evolution, of tampering with the genetic code. No.

These viruses evolved to replicate and use the human host’s machinery — which included the human host’s codon usage. There is absolutely nothing unusual in seeing a mix of codon usage especially in a virus which has recently switched hosts from one species to another (with possibly some intermediates in between).

Wade goes on to use the creationist language of improbability to argue against very natural evolutionary steps:

…a chain of events has to happen, each of which is quite unlikely for the reasons given above. A long chain with several improbable steps is unlikely to ever be completed….

This is exactly the argument creationists use to say why the eye could not have been evolved, or a human for that matter… nonsense. The POWER of evolution is exactly that — despite your fear that the argument can go too far… we have evolved using such rare sets of events.

Wade further argued that scientists are ignorant of codon usage frequencies:

…For the lab escape scenario, the double CGG codon is no surprise. The human-preferred codon is routinely used in labs. So anyone who wanted to insert a furin cleavage site into the virus’s genome would synthesize the PRRA-making sequence in the lab and would be likely to use CGG codons to do so….

If it was important for a particular codon to be used, virologists are very cognizant of which set, human or viral, should be used. Human-preferred codons are NOT blindly used, nor are they just routinely used in all labs. Codon usage is a conscious and important matter in molecular biology. Indeed, it may very well be that bacterial codon usage is actually the single most widely used preferred codon-set.

Then Wade tries to use a quote from a virologist to support his claims:

…“When I first saw the furin cleavage site in the viral sequence, with its arginine codons, I said to my wife it was the smoking gun for the origin of the virus,” said David Baltimore, an eminent virologist and former president of CalTech. “These features make a powerful challenge to the idea of a natural origin for SARS2,” he said….

NO — Baltimore is incorrect — there is no smoking gun!

If you’d like to read my thoughts on Biden’s newly announced 90-day investigation into the Origin of Covid in China, please click here.

Nicholas Wade, images are all used in accordance with Title 17 U.S.C. Section 107, commonly known as “fair use law”. This material is distributed without profit with the intent to provide commentary, review, education, and increase public health knowledge.

The post Debunking Nicholas Wade’s Origin of COVID Conspiracy Theory appeared first on Medika Life.

Here is an interview with a lawyer named Reiner Fuellmich showing what a full-blown hyperventilating fact-free attack looks like (please note: despite the introduction, the main body of the interview is all in English)

Going through his arguments is like shoveling the Augean Stables. But I’m no Hercules so I’ll focus on a very small but critical part of his argument, where Fuellmich tries to cast doubt on the polymerase chain reaction or PCR test. This is key because PCR is used to diagnose and track the COVID-19 disease and the SARS-CoV-2 virus that causes it.

What is Fuellmich saying?

Thanks to Robert Turner, we have a transcript of Fuellmich’s statements from that interview complaining about the PCR test:

[4:15] It [the PCR test] cannot be relied upon as it cannot distinguish between live and dead matter, meaning whatever tests positive to could very well be the fragments or remnants of your body’s own immune system’s fight against the common flu or the cold and it cannot tell whether a virus, and you need a whole virus, not just a fragment, whether a virus has entered your cells and is replicating because that’s the only way for you to become contagious.

[5:38]…you have to put this into a machine and then magnify it. This is called cycles of amplification, 2, 4, 8, 16, 32 and everyone agrees in the meantime that anything beyond 24 is unscientific. Apart from the fact, these tests cannot tell you anything about infection because they can’t distinguish between live and dead matter, but, if, if you go beyond 24 cycles, if you go for example to 34 cycles of application then you end up with at least 97% false positives, that’s what Mike Yeadon, former vice president of Pfizer told us.

Here I’ll focus on quickly laying down the facts to correct Fuellmich’s claims, and show where he is misleading people.

If you are interested in more in-depth primers on PCR, I have a couple posts here and here that I wrote for a friend who joined me in the lab doing biological research (including lots of PCRs).

Let’s break down Fuellmich’s comments piece by piece.

…It [the PCR test] cannot be relied upon as it cannot distinguish between live and dead matter…

Fuellmich tries to dismiss a test while displaying ignorance of what it does. First, a PCR test does not distinguish between living and dead. Second, being alive or dead has nothing to do with diagnosing COVID-19.

A PCR, or polymerase chain reaction, detects the presence of a defined genetic sequence by specifically amplifying it. That is the entire purpose of a PCR.

That genetic sequence can be encoded in DNA or RNA. In humans, our genetic information is permanently encoded in DNA, and transiently encoded in RNA. In some viruses like the one causing COVID-19, the genetic information is permanently encoded in RNA.

To detect RNA, such as that within the SARS-CoV-2 virus, an additional step transforms the RNA to DNA. This step is abbreviated RT (for reverse transcription). So, the test to detect COVID-19 is actually called an RT-PCR test.

The goal of PCR is to amplify, and therefore detect, specific genetic information encoded in either DNA or RNA.

PCR can, for example, detect the presence of a genetic sequence in tissue from a live person and one who has been dead for hundreds or even thousands of years. So, living and dead are irrelevant to the argument of PCR’s effectiveness.

Furthermore, being alive or dead has nothing to do with diagnosing COVID-19. The SARS-CoV-2 virus that causes COVID-19 does not even qualify as a living organism in many people’s opinions.

…whatever tests positive to could very well be the fragments or remnants of your body’s own immune system’s fight against the common flu or the cold…

Fuellmich displays complete ignorance of testing and biology in this statement. The RT-PCR test amplifies virus-specific genetic information. The RT-PCR test does not have anything to do with the patient’s immune system. The RT-PCR test does not detect anything specific to the patient at all.

Furthermore, testing has shown the RT-PCR test is so specific that it can distinguish the SARS-CoV-2 virus from other viruses including other coronaviruses.

The “common flu” is caused by several influenza viruses which are very different from the SARS-CoV-2 virus. Genetically and biologically, influenza and coronaviruses are very distinct classes and species. There is no possibility for the RT-PCR test to confuse the two.

The cold is caused by several human viruses including rhinovirus, several coronaviruses, influenza viruses, and others. Some of these belong to at least the same class of virus as the SARS-CoV-2 virus. However, the cold and COVID-19 viruses are all very different species. The RT-PCR test will not confuse any of them with SARS-CoV-2.

There are a couple recent coronaviruses which are much closer genetically to SARS-CoV-2, but testing has shown that the RT-PCR tests are able to distinguish between them. The one most closely related to the current pandemic virus is SARS-CoV, and one a little more distantly related is called MERS-CoV.

…it [PCR] cannot tell whether a virus, and you need a whole virus, not just a fragment, whether a virus has entered your cells and is replicating because that’s the only way for you to become contagious…

This statement is partially true, but is irrelevant to the logic and process of diagnosis, and irrelevant to the logic and process of public health.

The part of Fuellmich’s statement which is true is that the RT-PCR cannot distinguish between an intact virus, and free-floating viral RNA (perhaps what he calls “fragments”).

A clinical diagnosis of COVID-19 includes RT-PCR data as an important factor, but also uses clinical (symptoms) and exposure (who contacted whom) information as well. A clinical diagnosis requires multiple sources of information to increase confidence because treatments carry risks.

Public health does not try to make clinical diagnoses, but requires just enough data to suggest the spread of a virus. A positive RT-PCR result, whether the virus is intact or not, suggests that a transmission event (spreading from one person to another) has occurred. This spreading must be stopped quickly, and health officials must limit contact even before they have full clinical data.

…you have to put this into a machine and then magnify it. This is called cycles of amplification, 2, 4, 8, 16, 32 and everyone agrees in the meantime that anything beyond 24 is unscientific…

Again, a small part of this statement is true. During the RT-PCR test for COVID-19, the patient sample is put into what we call a thermal cycler, a machine which automatically heats and cools the sample according to a program in order to amplify (or make many copies of) a specific DNA sequence.

The detectability of the genetic sequence depends on how much DNA is there to begin with. If there is a lot of genetic material in the original sample, fewer cycles are required to detect its presence. If very small amounts of genetic material are present in the sample, more cycles are required. There is nothing about the magic number of 24 as being “unscientific”. The mere statement itself is unscientific, as it betrays a complete lack of understanding of the RT-PCR test.

RT-PCR tests routinely go into 40 or 50 cycles to amplify very small amounts of genetic material. Here is a graph of a typical RT-PCR to detect the SARS-CoV-2 virus, showing specifically that higher cycle numbers detect smaller amounts of RNA.

… if you go for example to 34 cycles of application then you end up with at least 97% false positives, that’s what Mike Yeadon, former vice president of Pfizer told us…

Again, there is a tiny kernel of truth in this statement, but which is highly distorted. In the RT-PCR test, the genetic sequence is detected when DNA is amplified enough for a fluorescent signal to be detected. The number of cycles required to obtain a detectable signal is called the Ct, or cycle threshold number. A very high Ct number is associated with false positives. However, the number Fuellmich gives, 24 and 34, are ludicrously low and incorrect.

Here is one of many papers which explains the Ct value, and some typical values of cutoffs for acceptable values:https://drive.google.com/viewerng/viewer?url=https%3A//www.publichealthontario.ca/-/media/documents/ncov/main/2020/09/cycle-threshold-values-sars-cov2-pcr.pdf%3Fla%3Den&embedded=true

This paper suggests a Ct cutoff of 40. Far higher than 24 cycles or 34 cycles Fuellmich cites as being “unscientific”.

There are many causes of false positive RT-PCR results, of which the RT-PCR’s Ct is only one:

Causes of False Positive SARS-CoV-2 RT-PCR Results

Contamination during

• Sampling (eg, an infected worker or surfaces; aerosolization of virus during collection)
• Extraction (eg, aerosolization in containment hood)
• PCR amplification
• Production of Lab Reagents (eg, manufacturers of the positive control may have contaminated other reagents produced in the same facility; contamination of other consumables)
• Contamination of the equipment by high viral titer specimens (eg, sample carryover)
• Cross-reaction with other viruses (eg, other coronaviruses)
• Sample mix-ups
• Software problems
• Data entry or transmission errors
• Miscommunicating results
• Variations in parameters around the LOD and definition of an indeterminate result
• Assuming that an indeterminate result is a positive
• Non-specific reactions

LOD, limit of detection; RT-PCR, reverse transcriptase-polymerase chain reaction.

(Table by Braunstein et al, 2021)

Conclusion

Fuellmich is engaging in a poorly-informed and dangerous campaign against public health measures such as vaccination, testing, and distancing. Even a cursory examination of RT-PCR shows how ignorant Fuellmich is of the process and capabilities of this important test.

Editors Note: For a complete dissection of Fuellmich’s Fiction, refer to this article

The post Getting the Story Straight on PCR… appeared first on Medika Life.