Scientific history of RaTG13
When the RaTG13 genome was published on January 27th I could not make any sense of the magic genome suddenly being published. I kept telling myself that it MUST have been published under a prior research designation and I am missing something! I eventually pieced together the actual story and it leads down a rabbit hole. For context, when hCoV-2019 was first being researched, many scientists believe the novel virus may have originated from a bat. The problem with this theory was that no Bat viruses were of “close” relation. In an early February 2020 publication, Dr. Shi Zhengli (the batwoman) and a team published a paper and out of nowhere simultaneously published the genome of a bat virus that is 96% similar to the novel virus, making this “out of thin air” genome the closest relative to hCoV-2019. But where did THAT virus come from? They claim it was from a 2013 sample but how is the scientific world just hearing about this in 2020? More importantly, this new “similar” virus is astonishing from a scientific perspective, as it makes SARS-CoV look tame. The internet went crazy with conspiracy theories. A very popular theory emerged stating that this sudden “new” RaTG13 is fake and does not exist. The conspiracy theory postulates that China and the WIV were attempting to cover their tracks and conjured this similar virus in order to peg hCoV-2019 to Bats in order to strengthen the argument of a wet market outbreak origin. While conducting thorough research on Bat coronaviruses I was able to eventually put all of the pieces together. The results are more shocking than the proposed conspiracy theories!
This is the story of the greatest beta coronavirus find in world history! Zheng-Li Shi and her team located an abandoned mining cave in Mojiang county, Yunnan province in southwest China. Expeditions were in August and September of 2012 as well as April and July of 2013. The team collected 276 samples from 6 Bat species. During their 4 expeditions, they discovered just 1 magical Rhinolophus affinis (RA) bat that contained an SL-CoV (SARS-Like Coronavirus)! While they discovered many viruses in the bats, only 1 contained a SARS-like virus.
*this table shows that the team discovered only 1 SL-CoV Ra sample
They sent their sample to Invitrogen in San Diego, USA and had them run amplification RT-PCR tests on a 440-bp fragment targeting RdRp to quick-match for SL-CoV (SARS-Like alpha and beta coronaviruses. Think of RdRp targeting as Customs scanning your passport. It tells them a good deal about you, but in reality, the information they are seeing is only a small part of who you are. The reason we run tests in this manner is to compare our findings in databases of known viruses. In this case, the team is looking for SARS-related viruses. Amplification of an 816-bp fragment extending the 440 bp was also performed. Spike genes were amplified using degenerate primers designed based on the alignment of known coronaviruses (sequences provided upon request). From the 138 positive samples, 152 RdRp partial coronavirus sequences (approximately 400 bp) were obtained, indicating co-infections of two viruses. Two sequences (HiBtCoV/3740-2 and RaBtCoV/4991) were homologous to beta coronaviruses, all other 150 sequences were homologous to alpha coronaviruses. The partial RdRp sequences obtained in their study were submitted to GenBank under accession numbers KP876505 to KP876546 and KU343189 to KU343200.
Everything checks out. I went and thoroughly reviewed every genome. All of these are partial RdRp samples collected from the six species of Bats and can be reviewed and aligned via GenBank.
*the SL-CoV-4991 phylogenic tree analysis of beta coronaviruses using the 440bp RdRp. This photo is showing us the relationship of this new virus compared to existing SARS-related beta coronaviruses. The top listing SARS-CoV-BJ01 is the original submitted genome of the 2002 SARS-CoV outbreak.
In their 2016 publication, they wrote something shocking that blew my mind; “Only two sequences detected in this study were homologous (naturally belonging) to beta coronaviruses. One of them (RaBtCoV/4991) was detected in a R. affinis Bat sample and was related to SARS-like-CoV. The conserved 440-bp RdRp fragment of RaBtCoV/4991 had 89% nt identity and 95% aa identity with SL-CoV Rs672 (Yuan et al., 2010). RaBtCoV/4991 showed more divergence from human SARS-CoV than other bat SL-CoVs and could be considered as a new strain of this virus lineage.”
*They are stating that they just discovered what appears to be an incredible virus. Recall that the RdRp sample is customs looking at your passport. Customs agents flag your passport and now the FBI is going to investigate you. The research team is clearly stating that this find warrants thoroughly research and testing.
Given how incredible this find actually was in 2013, the team would have subsequently sequenced the spike protein and the entire genome, before they published their findings in February 2016 research paper was published, right?
In order to understand the relevance of this discovery, let’s rewind to 2016! This new virus would be the most divergent, most incredible SARS-like coronavirus discovery in (beta) coronavirus history! This virus made SARS-CoV look tame and outdated! In 2016 essentially no one in the scientific community or in the world was unaware of these facts but, the Spike protein, and specifically, the Receptor Binding Domain of this virus are absolutely incredible! Research on this virus would warrant huge grants, fame, awards, honors, celebrity status for such an incredible discovery!
*Dr. Shi and her team had already spent years trying to find a Bat virus that could naturally a SL-CoV that had amazing hACE2 affinity. What does this mean? Let’s jump back to 2002. There is a SARS outbreak in Asia (and then in 30+ countries). A Bat with a specific virus somehow passed that virus to a wild cat (palm civet) and we humans then got the virus from the cat. This part is very important, no Bat has ever infected humans with a coronavirus. The SARS or SARS-related viruses in Bats does not have the ability to dock with our ACE2 receptors. In 2002 I could have been bitten by 50 of these SARS Bats and I would never get SARS. The palm Civet already had a mild virus and when the Bat infected the Civet, the virus from the Bat “mutated” into a form that COULD infect humans. This transfer is called zoonosis. After the SARS outbreak, many scientists were convinced that it was only a matter of time until these coronaviruses naturally mutated or evolved over time to the point where a Bat could directly infect a human and then the virus would indeed be able to dock with the human ACE receptor. That is an extraordinary idea and something that (we believe) has never happened in history. In 2013, Dr. Shi and her team worked on a joint venture with scientists at UNC to force this functionality. They created a Frankenstein chimeric virus just to prove that what they postulated was theoretically possible. By playing GOD with SARS the scientific community was outraged and scared. The part that does not make sense is that this 2013 4991 virus could already naturally dock with ACE2. In other words, they were searching for a needle in a haystack. They were not having luck so they went into a lab and synthesized the needle just to prove that it exists. Yet they also discovered the needle in the haystack..but never told anyone.
So there is zero chance the team did not sequence this genome and was unaware of the Spike protein of this incredible virus that could cause a worldwide pandemic. Back in 2013-2016 there is nothing that is even remotely close to this virus. It is on such an island of divergence that it is almost criminal to classify it with BetaCoVs.
Comparing the 440bp RdRp ORF1AB polyprotein to hCoV-2019 shows 1 amino acid differential in this partial sequence. Albeit a small part of the virus, no other virus matches our novel pandemic virus remotely close to this
In early February 2019, Dr. Shi’s team suddenly tossed a brand new genome online and published a paper, citing that hCoV-2019 must come from (horseshoe) Bats because it is so similar to this other sample obtained from Bats in July 2013.
*If an existing genome was already in the system and the new data was uploaded we would expect to see reference notes and that the previous listing had been removed or updated.
*The scientists were forcing an argument that this newly published genome (RaTG13) came from a Bat and is the closest relative to hCoV-2019, therefore our pandemic virus more than likely came from a bat.
At the time of this publication, there is quite literally zero record or publication referencing this sudden new virus that they designated as Bat SL-CoV RaTG13 (Ra being Rhinolophus affinis, 13 being sampling year). How could this new virus have been just ABSENT from the scientific community for SEVEN YEARS?!
In fact, there are (comparatively) barely any Rhinolophus Affinis Samples in our databases. Meaning there is a small pool or Bat viruses from this specific species. The team simply renamed the sample and maybe forgot that 4991 was already in GenBank?! Because 4991 is actually RaTG13, yet this super important publication which was read by all of the top scientists in the world makes zero mention of this important fact.
I ran an alignment of the 440bp RdRp ORF1AB polyprotein between the 2013 4991 submitted genome and this 2020 RaTG13 and it shows an identical match!
Now we have confirmation that RaTG13 (MN996532) is actually Ra4991 (KP876546)! We have confirmation that the RaTG13 virus is real and was indeed sequenced (RdRp) in 2013 and was referenced in a 2016 publication, clearly showing the virus is of high significance.
The rabbit hole gets deeper. China has a Bat virus database, which our teams frequently use for our research on Bat viruses.
In the photo above we see RaTG13 listed as MN996532
Yet RaTG13 is also listed as KP876546 and it clearly shows 4991 in the title name
Their February 2020 publication states:
“We then found that a short region of RNA-dependent RNA polymerase (RdRp) from a bat coronavirus (BatCoV RaTG13)—which was previously detected in Rhinolophus affinis from Yunnan province—showed high sequence identity to 2019-nCoV”
If she had just stated the name as 4991 and noted they updated the name to RaTG13, perhaps all of these conspiracy theories could have been avoided!
This chart shows all of the different proteins within coronaviruses and the % match scoring when comparing them to each other. This chart is showing that RaTG13 is off the charts unique
Now focusing on the biochemistry of RaTG13/4991, there are these interesting amino acid insertions within the Spike protein. Note the blue areas. These are unique insertions that are only also found in hCoV-2019 (listed as WIV04). These insertions are ONLY found in these two coronaviruses. A part of the Spike protein, the N-terminal domain contains these three unique insertions, listed as the first three sections in the photo. The fourth section should be ignored.
If the photo is too difficult to see, here are the exact chains where the mutations exist.
non-technical people should skip/ignore this
*Insertion #1 at position 72
RaTG13 (MN996532.1) NVTWFHAIHVSGTNGIKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
hCoV-2019 (MN908947.3) NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
*Insertion #2 at position 146. This is an interesting find as the KxxK motif appears, which can assist with affinity/virulency
RaTG13 (MN996532.1) NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE
hCoV-2019 (MN908947.3) NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE
*Insertion #3 at position 246
RaTG13 (MN996532.1) LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK
hCoV-2019 (MN908947.3) LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK
The three unique insertions in RaTG13/4991 are astonishing and would have made this the most incredible coronavirus ever found, had hCoV-2019 not appeared. That is how important this virus is. It is now being ignored since the pandemic is naturally the priority. Rather than conducting research on this virus, it is simply being sourced as PROOF that nCoV-2019 MUST be zoonotic. The discovery of Bat SL-CoV RaTG13 in 2013 makes every other discovery look pedestrian in comparison. This genome is so divergent to other Intermediate Horseshoe Bats that it would merit endless research. The ORF1ab and Spike (NTD, RBD) are extraordinary!
In my mind, the true conspiracy here is not publishing the astonishing findings of before 2020, be it with research papers or with publishing the complete genome. The fact that this information was withheld from both the public and the scientific community since 2013 should raise many alarms. The United States and China are/were both in possession of this research material and MUST have been conducting many studies on this virus and never produced any data after touting the importance of this virus in a 2016 publication. We the scientific community demand answers. For seven years this data was kept hidden until China was forced to publish the data only to use it as speculative proof for zoonotic origin.
*this post has been heavily revised to focus solely on RaTG13 and also to provide easier reading for the non-science community
Thanks for reading.
I am having trouble evaluating your posts.
Who are you? What is your background? When you assert that “this is true” to a mostly non-technical audience, why should we believe you? What do you know about this subject?
Thanks for some clarification
Fascinating info… Are you the source? Are you Dr. Mayer?
Unfortunately this subforum hardly has any activity — post it in the Current Events subforum to get more visibility.
I respect your right to privacy. Your screen name is wodz. You signed the post Dr. Mayer.
I did a quick google search and found the following.
If this is you I have the utmost respect for what you just posted. It is in another galaxy from my pay grade and thank you for putting your conclusions in layman’s terms.
There are other Dr. Mayer’s listed so can’t be sure it is you but thanks for your post and I would hope that you and Chris could get together and explore this further
Of course this virus smells of burnt rubber. I do not buy for a fact with all the “shenanigans” going on with Coronaviruses of bat origin, that this thing is of natural origin. Your supposition just adds to list of monkey business, that dose not pass the smell test and the science community as well as the public should demand explanations. I think there is enough on the subject to warrant a special independent investigation.
I think it’s fair to say that Peak Prosperity followers have been wondering why more people in the scientific research / virology community who have studied the Sars-Cov-2 (nCoV-2019) genome have not come forward with their analysis and conclusions as to whether the virus was lab manipulated, and its’ origin – for obvious reasons. Do you plan to publish your analysis, or any part of it? If not, why not?
I recognize that you have filled your post with diagrams and details but it is so difficult to follow for a non-technical person.I do recognize some of the nomenclature from reading the papers, but it is above my pay grade too.
Do you think you could diagram your history out? Maybe a flow chart of the various origins of the pertinent viruses and their salient features, followed by your theory on what parts of the SARS Cov-2 are derived from which sources.
Or perhaps a Powerpoint?
BTW, your post appears to be very thorough and I’m sure it took considerable time to lay out. Thanks for your efforts to educate us.
Replying to all. I am new here but had been watching Dr. Martenson’s videos for a while now. I am a virologist and biomolecular chemistry scientist from Munich, Germany. Not anyone fancy or important. I have been working with a few international teams focusing on the genome of this virus. I am also listed in the GISAID directory.
sandy_puppy: Regarding just the history of RaTG13 I was outlining the confirmed scientific history. We use certain databases to cross-reference viruses, especially to compare them. When this new nCoV-2019 virus emerged, there was nothing closely related to the virus, so it was a stretch to suggest the proximal origin was from a bat. On February 3rd, the first publication came out regarding the genome and structure of this new virus. It “appeared” that in this publication the scientists pulled a comparison virus out of thin air. A virus that both the public and scientific community had never seen before that was allegedly discovered in 2013. It turns out that virus (RaTG13) is a 96% match to nCoV-2019. In their publication, the scientists essentially said “well RaTG13 came from a bat..and this is close to nCoV-2019, therefore this new coronavirus more than likely came from a bat”. Many in the scientific community bought this without even questioning where this RaTG13 came from. In fact, dozens of publications cite this single virus as their PROOF that nCoV-2019 must have come from nature. Many in the conspiratorial world believed this RaTG13 does not actually exist, it is fake, or made up. My post was to fill in the gaps since it turns out there are a handful of people on earth that seems to know all of the details of this story.
tbp: Source? I hand wrote that entire post. I was unsure where to post things. I have moved this to Current Events. Thanks for the tip!
Mohammed Mast: Thanks for the reply. To remove any confusion I have updated my display name! I am a simple scientist from Germany.
nordicjack: The scientific careers of quite literally every single scientist around the world conducting GoF (gain of function) research is on the line. If there is a global consensus this was an engineered virus, we should expect grants to be removed, entire labs shut down, thousands would lose their jobs. This is the reason that countless scientists have stated “it is impossible this was man-made”. Declarative statements out of defense. The truth will eventually come out and thousands in the scientific community will lose their jobs.
jwhite: Same answer as above, speaking out could cost a career. On top of that, virtually no article is allowed to be published that even suggests anything other than the standard narrative. Back at the end of January, some Indian scientists published a pre-print publication on Elsevier suggesting that there is HIV homology within nCoV-2019. Their careers were essentially ended as the combined scientific community relentlessly attacked them. Higher-ups forced the paper to be taken down. In June other scientists began making the same discoveries.
Island Girl: That all sounds like a lot of work, lol. I tried to make the graphs large but the site seems to have restrictions. You should feel free to PM me if you have any specific questions about any bat coronaviruses.
Thanks to everyone. All of my posts tend to be 2+ pages as I am very detailed. It would be great to connect with Dr. Martenson at some point. I had emailed him months ago but never heard back. There appear to be some gaps in his knowledge, namely around docking receptors that I would be happy to pass along.
Thank you once again. It takes courage to step out in public the way you have on such a controversial subject.