The Zhang group of Fudan University have identified and validated two A-B intermediate SARS2 genomes from the early pandemic
This provides a key to understanding the origin of COVID19 🧵
A leak of polio from a research facility is indicated by a poliovirus genome sequence generated from a sample collected in 2014 in China by the Wuhan Institute of Virology
The sequence is 99 % identical to that of a polio strain from 1954 🧵
Our new paper describing the discovery of a novel SARS2 related coronavirus is out!
This coronavirus, which we term 'GX_ZC45r', bears signatures of genetic manipulation
We have uncovered evidence of undocumented GOF work in Wuhan 🧵
We have identified an infectious clone (IC) of a novel MERS-related coronavirus in rice sequencing datasets from Huazhong Agricultural University (HZAU), Wuhan
If they suspend Daoyu, who has done so much to investigate the Lab Leak hypothesis, they'll be coming for YOU next - if you dare to express an original thought....
When were the only two known pre-pandemic SARS2-related live isolates (attributed to pangolins) isolated ? And when were they sequenced ?
And why does one of them have SARS2 reads in its sequence file ? 🧵
@humblesci
Daoyu
@ydeigin
@quay_dr
and myself have published a study that shows the exclusion of 20 A/B intermediate SARS2 genomes from the analysis of Pekar et al. is unwarranted 🧵
Evidence for ‘live’ RaTG13 at WIV
Conclusion
Here, I conclude this series of threads demonstrating RaTG13 was generated from a bat transcriptome and not a fecal swab. This implies it was live cultured, contradicting public statements made by the scientists who worked with RaTG13
Apparently, pointing out the fundamentals of molecular evolution (that the SARS2 FCS didn't arise from nonsynonymous point mutations, but rather all available data indicates it is an insertion) gets you blocked !
Strange way to concede the point
41 logicians declare that forwarding a hypothesis 'harms' science
In the title they puzzlingly state the lab leak hypothesis is 'without evidence'
Comically, the Abstract immediately contradicts this by saying there is no 'strong evidence'
Which one is it ? 🤡
Why are virologists freely allowed to anonymize lethal synthetic viruses, but developers are put in jail for writing code that anonymize bitcoin transactions ?
Genetically enhanced infectious clones present a much higher risk than anonymous monetary transactions 🧵
Dr Rasmussen belongs to that peculiar tribe of experimental biologists who claim deep insight into bioinformatics analysis, yet has never done a Blast search
Our data is robust to replication
What was the restriction enzyme BsmBI, itemized in the DEFUSE budget, to be used for? 🧵
3 possibilities:
i) To make an spike ectodomain expression vector
ii) To insert recombinant S genes into VRP vectors
iii) To make infectious clones (ICs)
In their survey of the Huanan Seafood Market, Liu et al conclude that there is no evidence for a zoonotic transmission of SARS2 at the market
Out of curiosity, I did a deep dive into sample Q61 (Env_0576), which they report as having a high proportion of raccoon dog reads 🧵
Was Baric aware of the work on the human α-ENaC furin cleavage site (FCS) at the University of North Carolina (UNC) ? 🧵
In a striking coincidence, the human α-ENaC FCS is exactly the same as that of SARS2, as first noted by Anand et al in 2020
14/ In summary, our results indicate that a novel, unreported SARS2-related coronavirus has recently been subject to genetic manipulation in China. These activities are of great potential concern in terms of Biosafety, and the surveillance of Gain of Function research
2/ Chesnais et al sequenced 3 poliovirus genomes recovered from 60 year old historic samples generated by Albert Sabin at the Pasteur Institute, Paris
Sabin is the father of the oral polio vaccine, created from attenuated polio strains
Despite emerging in Wuhan, the city with the most expertise in tracing coronavirus outbreaks in the world, there is still no sign of an intermediate host for SARS2
The likely intermediate host for SARS1 (palm civet) was identified just months after the initial outbreak
I've identified numerous vertebrate RNA viruses in the Q61 raccoon dog sample from Liu et al's survey of the Huanan Seafood Market
Their % genome coverages are substantially higher than that of SARS2, and many are associated with animals identified previously in the dataset 🧵
🚨BREAKING🚨
EcoHealth Alliance President Dr. Peter Daszak will testify at a public hearing on May 1, 2024.
Dr. Daszak must answer questions about COVID-19 origins, dangerous gain-of-function research, and his relationship with the Wuhan Institute of Virology in China.
What is the true trace level of SARS2 in the raccoon dog sample Q61 from the Huanan Seafood Market ?
Here, in a refined analysis, I show that human common cold coronaviruses are present in quantities greater than SARS2 in Q61 🧵
🚨BREAKING🚨
EcoHealth Alliance President Dr. Peter Daszak ADMITS "of course" the Wuhan Institute of Virology could have hidden coronaviruses.
Dr. Daszak also does "not know" if the CCP deleted any coronavirus sequences or samples.
Another top public health official, this time Dr Deborah Birx, thinks SARS2 escaped from a Wuhan lab
Dr Birx is an infectious diseases expert and former presidential COVID19 advisor
Differential gene expression analysis of the controversial RaTG13 dataset reveals strong similarity to the RaTG15 dataset, also described as generated from a Rhinolophus affinis 'rectal swab' from the Mojiang Mine
This indicates they have a common, undefined source 🧵
@jbkinney
First, you’ve not shown an evidence that COVID wasn’t natural. Bold assumption. Even if it was, it’s a once in a generation fuck-up while thousands of virology and GMO labs have operated safely for years. See why the people operating them are pissed off? You need to clam down.
Dear oh dear, I thought I was being constructive by pointing out
@stuartjdneil
's numerous factual errors
Puzzling he would take offence, as he likes to point out the errors of others with gusto (and nothing wrong with that)
3/ Poliovirus is a single stranded positive sense RNA virus, that only naturally infects humans (no other natural hosts are known)
There are 3 poliovirus serotypes: PV-1, PV-2 and PV-3
Bombshell !
From an early draft of DEFUSE:
"The BSL-2 nature of work on SARSr-CoVs makes our system highly cost-effective relative to other bat-virus systems"
You may have heard that a research proposal called DEFUSE lays out a blueprint for the creation of COVID.
You may also know that other scientists brush off DEFUSE because the risky virology was to take place in North Carolina.
Today new docs obtained by me indicate American
Low levels of bacteria in the 'rectal swabs' used to generate 7896 clade sarbecovirus genomes 🧵
On the trail of the true identity of RaTG13 I decided to look at the 7876 clade NGS datasets (which include RaTG15), as these were also generated from the Mojiang mine....
18/ In conclusion, there is nothing to link the SARS2 sequences to raccoon dogs in particular, out of all the animals detected, and its low level in the sample is consistent with other human coronaviruses also present at the Huanan Seafood Market
Daszak claims to have discovered a bat CoV from Thailand with 'almost' as much potential to infect humans as SARS2
No mention of a FCS
Disturbingly brags about doing the labwork at BSL2
This statement about DEFUSE by Eddie Holmes is misleading. DEFUSE describes the identification of potential FCSs in the spike gene of SARSr-CoVs. FCSs are typically found at the S1/S2 boundary...... 🧵
Baric : "we were fundamentally interested in why didn't sarbecoviruses have a furin cleavage site"
It's because there is no (natural) selection for an FCS
They may also be maladaptive in a natural environment
h/t
@Rebecca21951651
We have uncovered evidence of undocumented GOF work in Wuhan 🧵
We have identified an infectious clone (IC) of a novel MERS-related coronavirus in rice sequencing datasets from Huazhong Agricultural University (HZAU), Wuhan
Our new paper on intermediate lineage A-B SARS2 genomes is out !
Within, we criticize the exclusion of 20 potential A-B intermediate genomes from Pekar et al (2022), finding that the majority were improperly excluded 🧵
We have discovered 6 more A/B intermediate SARS2 genomes (with C/C genotype) from Wuhan 🧵
This is in addition to the 7 new intermediates (also C/C) we previously identified from Sichuan 👇
We have discovered 5 more A/B intermediate genomes from Sichuan (with a C/C genotype), in addition to 2 we found previously 🧵
These were not considered by Pekar et al, despite 2 of the 5 conforming to their inclusion criteria 👇
@WashburneAlex
I had one manuscript rejected on the basis that it might cause a terrorist attack (no kidding)
I had no idea network analysis was so controversial, shows what fragile times we are living in 🙃
17/ 3) This indicates a date of emergence of no later than ~ Oct 2019, as per Kumar et al
This is based on the number of mutations needed (3) to get to proCoV2 from the lineage B reference sequence (Hu-1)
6/ Surprisingly, the Glenn genome showed 95 % identity to WIV14, generated from a sample collected in Dec 2014 by the Wuhan Institute of Virology (WIV)
WIV14 (accession KY703697) was isolated in Vero cells. from a child in Anhui, China, described 👇
NIH deleted two Pangolin metagenomic datasets on March 16 2020 at the request of Kangpeng Xiao of South China Agricultural University
Inadvertantly revealed by a FOIA request filed by Empower Oversight
Mitochondrial rRNA analysis of the SARS2 contaminated Antarctic datasets identified by Csabai and Solymosi 👇
I ran Metaxa2 on the SARS2 contaminated datasets, then assembled the mit SSU rRNA reads using megahit to produce contigs
Deliberately misleading. The clue to Marburg virus's origin is in its name 'Marburg', a town in Germany. Marburg virus is found in monkeys and monkeys are not native to Germany
Why is
@angie_rasmussen
still trying to claim that the 1967 Marburg outbreak was caused by zoonosis, rather than a lab leak? It goes to show that many virologists will insist that an outbreak started by lab acquired infections is actually a zoonosis.🤦♂️
22/ To conclude, it appears highly likely that WIV14 was the result of a leak from a scientific facility
Its 'frozen' sequence is reminiscent of the Russian H1N1 flu genome, which was also likely released from a scientific facility
An oft-repeated fallacy is that the BANAL viruses are more closely related to SARS2 than RaTG13, now repeated in the article in SciAm by
@stuartjdneil
@STWorg
@past_is_future
We have discovered 5 more A/B intermediate genomes from Sichuan (with a C/C genotype), in addition to 2 we found previously 🧵
These were not considered by Pekar et al, despite 2 of the 5 conforming to their inclusion criteria 👇
I have published a paper on my analysis of the RaTG13 dataset
RaTG13 is the closest phylogenomic relative of SARS2
Transcriptome and GO enrichment analysis indicates the likely source of the dataset is a bat mating plug, rather than a fecal swab 🧵
10/ One of the things deeply concerning about this research team is that ZLS's close collaborator Yigang Tong thought that culturing novel PPPs in BSL2 labs and observing if anyone got sick was a good way to assess if the PPP was pathogenic to humans !
h/t
@BillyBostickson
Dr Debarre declines to replicate our analysis reporting the discovery of a genetically manipulated MERS-related infectious clone from Wuhan, and prefers to dismiss it out of hand
Probably because she knows our analysis is robust
December 18, 2023
Statement On New Revelations About “Project DEFUSE”
Documents reported today by U.S. Right to Know reveal that the president of EcoHealth Alliance, Peter Daszak, planned in 2018 to use U.S. Department of Defense funds to perform high-risk virus experiments at
9/ Bat HKU4r-CoVs are potential pandemic pathogens (PPPs), with the potential to infect human cells 👇 The leak of this material into a rice sequencing dataset indicates serious biosafety violations in Wuhan
@R_H_Ebright
@HansMahncke
They claimed political reasons aka 'international harmony', but this was likely a smokescreen to cover for their real anxiety - that their reckless role in funding dangerous research in Wuhan might be revealed
I am sure
@STWorg
will be horrified to discover the error in his SciAm article and will want to correct the record, especially given his academic interest in the spread of 'misinformation'
4/ The 3 genome sequences were from strains Glenn (PV-3), cold variant P2149 (PV-1) and cold variant P712 (PV-2)
Glenn was a cold adapted strain isolated before 1956 from a child in Cincinnati
Evidence for ‘live’ RaTG13 at WIV
Part 1
Over the course of several threads, I will present evidence that the genome of RaTG13, the closest relative of SARS2, was not generated from a fecal swab as claimed but a ‘live’ isolate.
Unravelling the RaTG13 Dataset's Origin
The RaTG13 dataset has overexpressed transcripts which indicate it was mis-sampled from a bat mating plug
This provides a reasonable explanation for anomalies in the dataset, described as a 'fecal swab' 🧵
11/ WIV14 should be more divergent at the sequence level if it had been in circulation for 60 years after splitting from Saukett A
The most plausible explanation is that its progenitor was in storage for a substantial amount of time, and then released into the population
🚨Today is the day🚨
EcoHealth Alliance President
@PeterDaszak
appears for a transcribed interview.
What does Dr. Daszak know about the origins of COVID-19 and dangerous gain-of-function research at the Wuhan Institute of Virology?
Americans are ready for answers!
5/ The P712 cold variant was a serially passaged derivative of strain P712. P712 is a constituent of the oral polio vaccine
The P2149 cold variant is likewise a serially passaged derivative of strain P2149
Both cold variants are able to grow at 25C
Evidence for ‘live’ RaTG13 at WIV
Part 3
In two previous threads, I have presented evidence the genome of RaTG13, the closest relative of SARS2, was not generated from a fecal swab as claimed. In this thread I examine whether RaTG13 was generated from a mislabelled oral swab
6/ The vector was subsequently used in a paper by Linfa Wang and Zhengli Shi to make a non-infectious SARS clone. ZLS is China’s leading coronavirologist and director of Center for Emerging Infectious Diseases at the Wuhan Institute of Virology (WIV)
8/ Saukett A was first obtained from a child, James Sarkett (the name of the strain was misspelled), in California prior to 1954 by medical pioneer Jonas Salk, creator of the IPV
Salk never received a Nobel for his work, but perhaps should have done
The CGG arginine codon, although being extremely rare in coronaviruses is found in the SARS2 FCS insert
It turns out to be a popular choice for synthetic coronavirus sequences
@flodebarre
@mbw61567742
@Ayjchan
It is clear that CGG is loved by many genetic engineers: Moderna has recoded 39 of the 42 SARS2 spike arginines by CGG while Pfizer has recoded 19 of 20 CGx spike arginines by CGG.
From
@COVIDSelect
's letter to Dr Peter Daszak
"This comment appears to be materially inconsistent with your testimony assuring the Committees that the proposed work was planned to be done exclusively at UNC"
h/t
@emilyakopp
@USRightToKnow
10/ Of great concern is the presence of reads corresponding to the MERS receptor binding domain (RBD) spliced into the HKU4r-HZAU-2020 backbone (which we term HKU4r-HZAU-2020+S(MERS). This indicates a second IC is present and represents a GOF chimera of the most lethal kind
Tabak: "The origin of SARS-CoV-2 has not been identified, despite intensive efforts"
Give me a break, NIH has put zero effort in investigating a lab origin, instead preferring to smear investigators
10/ The high sequence identity, with only 70 nucleotide differences, indicates a recent common ancestor between Saukett A and WIV14
However, Saukett A was isolated < 1954. Given the high mutation rate of polioviruses, the high sequence identity is anomalous
A new critique of Pekar et al's simulations published by
@nizzaneela
on PubPeer
A bug-fix significantly reduces confidence in the authors' finding of two spillovers...
9/ The Saukett A genome showed a 99% match to the WIV14 genome, providing a closer match than Glenn
This can be seen on the tree below (genetic distance is indicated by branch lengths)
New paper by
@jbloom_lab
explores 5 animal CoVs detected in the Huanan Seafood Market
In samples collected Jan 12 2020, 4 CoVs are more substantially more abundant than SARS2, and 3 show strongest associations with their putative host animals 🧵
I have performed additional new analyses comparing SARSCoV2 to other animal CoVs in environmental samples from Huanan Market
Paper w these new analyses is & full computational pipeline at
The new results are summarized below.
23/ Another example of 'frozen' sequences is that of hand, foot and mouth disease (HMFD) strains sampled in 2007-2009 from China, which bear high identity to the BrCr prototype strain sampled in 1970 USA, indicating a likely lab leak origin
7/ As Glenn is related to Saukett A (PV-3), which is used to produce inactivated polio vaccine (IPV), the group also sequenced the Saukett A genome
They obtained a sample from the British National Institute for Biological Standards and Control (NIBSC)
More scintillating logic from the 'you're harming science by proposing a hypothesis we don't like' crowd
Now predictably morphed into 'you're killing people'
8/ The sequencing data deposition date of 19 Jan 2020 is significant, as it indicates that this work was done prior to the beginning of the SARS2 pandemic
A potential explanation for the alanine (A684) in the SARS2 FCS ?
Alanine mutational scanning is used to systematically mutate residues in functional sites, to determine if they ablate function, so indicating their importance 🧵
"Débarre’s tactics include exaggerating minor discrepancies, framing routine scientific practices as ethical breaches, and publicly attacking Bloom to undermine his credibility. These actions ... suggest a calculated effort to damage Bloom’s reputation"
25/ Finally, another intriguing example of a 'frozen' sequence is that of the 2021 Ebola outbreak in Guinea. The genome sequence was little different from 2014 sequences from the same region
I made a codon usage table of the plasmid spike discovered by
@MartinaSisters
🧵
A priori, the sequence can be seen to be strongly optimized, given its extreme codon usage bias
@debralex57
@mkeulemans
@19961995sw
@volkskrant
For example, the Wuhan Institute of Virology had a 2017 grant to use infectious cloning to make recombinant SARS coronaviruses. The results of this are unknown. Currently they refuse to share their records with WHO or the NIH.
Incredible that we still don't know what live isolates the WIV had in their possession
In the absence of direct access to WIV researchers, perhaps their close collaborators Eddie Holmes and Ralph Baric might have some relevant documentation
I have a feeling that in future Kevin’s work will be seen as having been pivotal in alerting the public to the massive dangers of public health by fiat and uber-centralization
Another blow against the Huanan market
No SARS2r CoVs found in animals, including raccoon dogs, "captured by local traders in rural areas of Wuhan for vendors in animal markets including the Huanan Seafood market"
Yong-Zhen Zhang's new paper analyzing animal samples collected around Wuhan in early 2020 for CoVs is in
@VirusEvolution
(). Recall his group also reported the first human
#SARSCoV2
sequence. (1/3)
The microbes present in the SARS2-contaminated Antarctic soil datasets discovered by Csabai/Solymosi can help to better understand the nature of the SARS2 contamination 🧵
7/ The cloning scenario is supported by the presence of the commonly used E.coli pUC57 cloning vector at the 5' end of one of the GX_ZC45r reads
This indicates cloning of virus genome fragments, and concomitant amplification - a common step in making infectious clones
24/ Venezuelan equine encephalitis virus (VEEV) strains isolated in 1995 also have 'frozen' sequences, showing striking genome identities to strains isolated 1962-64
The 1995 strains likely derived from a leaked 1962-64 strain used for vaccine production
A mysterious addition has been made to Worobey et al and Pekar et al in Science
Full of strong statements regarding issues that have not been settled (highlighted)
The vibe I am getting from this is 'the beatings will continue until morale improves'