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2. INVESTIGATION OF RaTG13 AND THE 7896 CLADE

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This is the second part of a series of reports based on our previously unpublished investigations into the origins of SARS-COV-2. We wish to thank all the independent researchers who have contributed to this investigation, especially members of the DRASTIC Collective, many of whom wish to remain anonymous for reasons of security and privacy.
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INVESTIGATION OF RaTG13 AND THE 7896 CLADE
Annotated Map courtesy of Brian Reed
William Bostickson and Yvette Ghannam (2021)
This is the second part of a series of reports based on our previously unpublished
investigations into the origins of SARS-COV-2. We wish to thank all the independent
researchers who have contributed to this investigation, especially members of the DRASTIC
Collective, many of whom wish to remain anonymous for reasons of security and privacy.
TABLE OF CONTENTS
1 ANOMALIES IN THE ORIGIN OF RaTG13
2 ALLEGED ANOMALIES IN RaTG13 SEQUENCE DATA
3 QUESTIONS ABOUT THE RaTG13 PUBLICATION TIMELINE
4 ANOMALIES IN THE AMPLICON DATA PUBLICATION TIMELINE
5 WHAT IS THE 7896 CLADE?
6 QUESTIONS CONCERNING RaTG13 AND THE 7896 CLADE
A. RaTG13 FAECAL SAMPLE
B. RaTG13 SEQUENCE DATA
C. QUESTIONS ABOUT THE MOJIANG MINERS PNEUMONIA CASES
D. QUESTIONS ABOUT THE 7896 CLADE
E. OTHER RELATED QUESTIONS
7. CONCLUSION
8. REFERENCE LIST
1. ANOMALIES IN THE ORIGIN OF RATG13
The pressing need for an independent forensic investigation into laboratories in
Wuhan is highlighted by the lack of transparency and obfuscation regarding both the origin of
the closest known relative of SARS-CoV-2, RaTG13, and its published sequence data, as
discussed below.
Several different theories have been proposed to explain how a SARS like virus
whose closest known “relative”, RaTG13, was obtained from an abandoned mineshaft in
Tongguan, Mojiang, Yunnan in 2013 (Ge et al., 2016), could emerge into the human
population in Wuhan 6 years later and 1100km away. These theories range from flawed
claims of recombination between ancestral strains of related bat betacoronaviruses in
microbats and megabats in the Karst formations of Yunnan (Gallaher, 2020) to recent
surprising claims that mink in NE China were involved (Zhou & Shi, 2021). As
recombination of viruses between megabats and microbats have not been witnessed
previously and there are no mink farms in Yunnan, let alone bats carrying viruses similar to
SARS-CoV-2 in NE China, both these claims have been dismissed by experts (Everington,
2021).
More evidence based studies focus on similarities between the symptoms and clinical
evidence from SARS-CoV-2 and a 2012 “Mojiang Miners Pneumonia” Illness (Rahalkar &
Bahulikar, 2020a). Anon (2020) focuses on the subsequent bat sampling activities undertaken
in the same mineshaft, while Latham & Wilson (2020) indulge in extended conjecture to
support their particular theory.
The mine where the closest known relative to SARS-COV-2 was collected in a
sampling expedition by WIV was never revealed by the Chinese authorities and attempts to
visit it have been blocked by local residents and the police. It was located by DRASTIC
Team members from map research, Chinese texts and narrative accounts: See Figures 1, 2
and 3 below.
Figure 1. Chinese texts and narrative accounts Source: Google Translate
(Francisco A. de Ribera).
Figure 2. Details of “Benping” abandoned Copper Mine Location in Tongguan, Mojiang,
Yunnan, China. Source: Brian Reed @Drinkwater5Reed.
Figure 3. (蚌平铜厂(地片) Bengping Copper Factory (abandoned site) Source: Francisco
A. de Ribera
From the research discussed above, three conditions the location of the mine must
meet are that it must be: In Bengping valley (white contour) - Closer to Danaoshan than
to any other town (to the left of purple line, and below blue line) - At 3.5 km (+/- 0.1
km) from Sankezhuang, to the N +/- 22.5º, see Figure 4 below:
Figure 4: Benping Map Source: Francisco A. de Ribera.
The three theories mentioned earlier are all based on a 2013 Master’s thesis (Xu,
2013) discovered by a member of the DRASTIC Investigation team (Colaiacovo, 2020b,
Gartland, 2020), which discusses the case history of six local miners tasked with clearing bat
guano from an abandoned copper mine in in Tongguan, Mojiang, Yunnan province in 2012.
The six miners became sick with a SARS related pneumonia which was never reported to the
WHO, despite Chinese and WHO regulations, despite the fact that three died and three
survived (50% fatality).
The Kunming Institute of Zoology confirmed that the patients had been exposed to
horseshoe bats (Yua et al., 2019), while the medical thesis concluded that it was "a Sars-like
coronavirus from a horseshoe or other bat species”. This was partially confirmed at the time
by The Wuhan Institute of Virology after they analyzed the serum IgM from one of the
miners. Finally, Dr. Zhong Nanshan, China’s top expert on SARS, participated in the
sampling and confirmed that the resulting disease appeared to be viral (Xu, 2013).
These facts were further confirmed in a Ph.D. thesis (Huang, 2016) again discovered
by the DRASTIC investigation team (Colaiacovo, 2020b, Gartland, 2020) which was
supervised by Dr. George Gao Fu, Director of the Chinese CDC. Rahalkar & Bahulikar
(2020b) refute Zhengli Shi’s surprising claim that the illness was caused by a fungal
infection (Qiu, 2020), as anti-fungals failed to remedy their condition and the observed
vascular complications, elevated D-dimer, thromboembolism, elevated SAA (serum amyloid
A), low levels of lymphocytes as well as CT scan data, “all point towards primary viral
pneumonia” (Rahalkar & Bahulikar, 2020b). Indeed, the Wuhan Institute of Virology itself
originally confirmed that the serum IgM from one of the miners indicated a viral disease (Xu,
2013).
Although Zhou et al. (2020b) published an “Addendum” on 17 November 2020 which
attempted to clarify some of the above concerns about RaTG13, claiming that they had found
no SARS- coronaviruses in the serum samples of the Mojiang miners kept by WIV,
supporting data for these claims was not provided and the addendum itself seems not to have
been peer reviewed. This lack of data and professionalism unfortunately raises further
significant questions about the reliability of Zhou et al.’s (2020) research (Suryanarayanan,
2020d).
2. ALLEGED ANOMALIES IN RaTG13 SEQUENCE DATA
Several researchers have challenged both the authenticity of RatG13 sequence data
and the circumstances surrounding its submittal. Multiple concerns have also been raised
concerning the legitimacy of RaTG13 and its corresponding paper (Zhou et al., 2020). Singla
et al. (2020) question the experimental procedure used, poor data quality, lack of
reproducibility and contamination issues. Both Signus (2020) and Rahalkar & Bahulikar,
(2020c) criticize RaTG13’s corresponding paper (Zhou et al., 2020) due to perceived
anomalies in the Fecal Swab Data and question the legitimacy of the RaTG13 metagenomic
dataset on the grounds that the fecal sample lacks bacterial read. Lin & Chen (2020) found
anomalies when comparing the guided assembly of RatG13 to Wuhan –HU-1 which again
suggested evidence of contamination, leading them to criticize both the quality of the
corresponding paper and dispute the identification of RaTG13 itself.
Zhang (2020c) and Rahalkar & Bahulikar (2020c) discuss several anomalies in the
sequence data of RaTG13 involving sample contamination, amplicon sequences and levels of
bacteria found. Zhang (2020b) questions how RaTG13 was identified under the described
methodology, the poor quality of the data, incomplete sequence data, incoherent structures
and the experimental procedures described in the original paper by Zhou et al. (2020).
Specifically, the SRA data fails to match the reference genome, revealing gaps, a different
consensus, different bases and two sites in the raw data which fail to match the published
RaTG13 genome sequence (Zhang, 2020c).
Furthermore, the three different versions of the RaTG13 sequences, Ampliseq,
GenBank and mNGS contigs, uploaded as GenBank accessions: MN996532.1, SRX7724752
and SRX8357956 reveal inconsistencies:
The fecal sample sequence mNGS data uploaded reveals many unrecognizable repeat
sequences with no bacterial reads (Rahalkar & Bahulikar, 2020c).
The Sanger Amplicon data was uploaded months later in order to fill in the observed
gaps in the sequence data, with the final four amplicons characterized by the presence
of DNA synthesis assembly error signatures, suggesting the involvement of cell
culture (Zhang, 2020c).
The SRR sequence data fails to coincide with the putative host of RaTG13, the bat
species Rhinolophus Affinis (Ra), instead revealing surprising levels of eukaryotic
contamination.
More disturbingly, RaTG13 reveals traces of Human ERV and HIV-1 derived
material possibly from gag lentivirus artefacts which suggest that RaTG13 itself was
the result of cell culture (Zhang, 2020c).
One possible interpretation of some of the identified anomalies of RaTG13 is that it is
some kind of artefact sequence based on a combination of eight unpublished SARS-COVs
from the Ra7896 Clade. The RdRp sequences of the 7896 clade were published in June 2020,
but until Zhou et al. (2020) clarify their data and methodology, the aforementioned concerns
remain.
While, some of these concerns were partially addressed by Eldholm & Brynildsrud
(2020), their paper failed both to satisfy the major criticisms regarding RaTG13 (Lin & Chen,
2020; Singla et al., 2020; Zhang, 2020c) and to quash increasingly vociferous demands
(Signus, 2020) for Zhou et al. (2020) to publish all their data and to share samples (now
allegedly no longer available) for independent verification, as well as clarify the precise
methods used to obtain the genome sequence, especially the sample processing protocol
(Rahalkar & Bahulikar, 2020c)
As discussed above, there is some evidence that RatG13 is in certain ways a
laboratory “construct" rather than a viable virus (Zhang, 2020c). This is backed up an
increasing consensus that RatG13 is not efficient at infecting animals or cells, despite some
ambiguous results from computer models & pseudoviruses, which is supported anecdotally
by the failure of Shi Yi, a researcher at the CAS Institute of Microbiology in Peking
(Mallapaty, 2020) to infect animal species with an inactivated strain of RaTg13 in order to
explore its mutation patterns compared to SARS-COV-2.
Despite claims that RaTG13 emerged from bats and the observed similarities with
SARS-COV-2, so far experimental data has not shown that RaTG13 is able to infect most bat
species (Liu et al., 2020). Surprisingly few successful in vivo experiments have been carried
out to test its ability to infect different animals. In April 2020, a paper claimed that "a wide
range of ACE2 orthologs support binding to RBD proteins of Bat-CoV RaTG13", however it
was later revealed that the authors had used the wrong species of bat for the ACE2 sequence
(Rs instead of Ra) thus invalidating the claim (Li et al., 2020). Another experiment found
that RaTG13 viral protein was so unstable when the researchers tried to express it in mammal
cell lines, that they were forced to use chemical cross-links to generate particles for analysis
when they prepared the EM grids (Wrobel et al., 2020).
Finally, Wang et al. (2020) were so surprised by the high synonymous divergence
level (1.0366) shown by RaTG13, considering that it was the earliest sampled sequence, that
they initially considered the possibility “that RaTG13 has been maintained under conditions
which have allowed it to continue to evolve after its initial sampling”!
3. QUESTIONS ABOUT THE RaTG13 PUBLICATION TIMELINE
Zhou et al. (2020) originally claimed in their paper, which was received on 20 January
2020 before publication on 3 February 2020, that they had identified the closest matching
relative to SARS-COV-2 from the RdRp of BatCov 4991 (later renamed RaTG13) which was
an unpublished sequence from the WIV database:
"... a short region of RNA-dependent RNA polymerase (RdRp) from a bat coronavirus
(BatCov RaTG13)which was previously detected in Rhinolophus Affinis from
Yunnan provinceshowed high sequence identity to 2019-nCoV. We carried out full-
length sequencing on this RNA sample"(Zhou et al., 2020a)
Surprisingly, Shi's 2020 paper (Zhou et al., 2020a) did not cite her own paper that
described the original discovery of RaTG13. However, a different group of researchers in
Wuhan (Chen et al, 2020) did cite it in their paper received on 27th January 2020:
Phylogenetic analysis indicates that 2019-nCoV is close to coronaviruses (CoVs)
circulating in Rhinolophus (Horseshoe bats), such as 98.7% nucleotide identity to
partial RdRp gene of bat coronavirus strain BtCoV/4991 (GenBank KP876546, 370 nt
sequence of RdRp and lack of other genome sequence)”
Peter Daszak, President of EcoHealth Alliance, who was a close collaborator with
WIV’s emerging virus group, claimed that RaTG13 was only sequenced for its RdRp in 2013
and left in a freezer at the WIV lab in Wuhan for six years until the current pandemic began.
He denied that it had been sampled or experimented on since 2013 in an interview with Vox
(Barclay, 2020)
"No one [in Wuhan] cultured viruses from those samples that were 20 percent different, i.e.,
no one had SARS-CoV-2 in culture."(Barclay, 2020)
Cattaneo (2021) highlights the revisions detected in accession numbers of RatG13 on
GenBank, and points out that there is no available evidence of any submission of RaTG13’s
viral genome earlier than 2020, despite the GISAID documented sampling date in 2013,
which in turn has raised “questions in the scientific community about the origins of the
first isolates of the RatG13 coronavirus” (Cattaneo, 2021). He concludes that Zhou et al.
(2020) should help clarify questions about RaTG13 with a view to improving understanding
of the evolution of SARS-CoV-2.
4. ANOMALIES IN THE AMPLICON DATA PUBLICATION TIMELINE
The original sample sequence data for RaTG13 was uploaded under filenames
“Sars_SL3_R1_171127” and “Sars_SL3_R2_171127” on 13 February 2020:
https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP249482
Then, on May 19, 2020, a researcher from WIV kindly uploaded the sequencing data of
RaTG13 dating back to 2017 and 2018:
https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR11806578
https://www.ncbi.nlm.nih.gov/sra/SRX8357956
An independently reviewed list of the names of the reads of the amplicon sequences of
RaTG13 which were uploaded can also be seen in Anon (2020). This data revealed that,
contrary to the original claims of Zhou et al. (2020), the Spike Protein of RaTG13 was actually
sequenced in 2018. In fact, the amplicon data shows that WIV had begun resequencing
RaTG13 in 2017, directly contradicting both Peter Daszak’s claim that it had been left in a
freezer for 6 years (Arbuthnot et al., 2020; Barclay, 2020), and Zhou et al.’s (2020) original
claim.
The uploaded date revealed that the RdRp and Orf8 of RaTG13 were in fact sequenced in
June 2017 and the spike protein in late 2018. This was likely due to the discovery of more
closely related viruses in September 2018 (Hu et al., 2018) which facilitated improved primer
design (Lucey, 2020).
The dates in the amplicon sequences and swab sequence filenames show a pattern of
consistent with their other studies on bat betacoronaviruses, in that WIV began with fecal
sampling in 2013, then published the RdRp in 2016, followed in 2017 by sequencing around
the RdRp and illumina sequencing in late 2017, finally sequencing the remaining amplicons
in 2018.
After questions were raised by several independent researchers from the DRASTIC group
(Colaiacovo, 2020b ; Gartland, 2020) about the raw sequencing data of RaTG13 uploaded in
May 2020, Zhengli Shi finally clarified in an email interview with Jon Cohen of Science
Magazine in July 2020 that WIV had actually managed to almost completely sequence
RaTG13 in 2018 (Cohen, 2020).
Zhengli Shi also mentioned in the Science interview that RaTG13 was missing “15nt
from the 5' end”, but how could she know that 15 nucleotides were missing from the 5' end,
as this was months before she published the updated sequence with the extra 15nt (without
the usual raw data to support it). Clearly, she must have had more data that she failed to
share to know that it was missing exactly 15nt, as although the sample had “disintegrated”,
the sequence data must have been available.
In 2018, as the NGS sequencing technology and capability in our lab was improved, we
did further sequencing of the virus using our remaining samples, and obtained the full-length
genome sequence of RaTG13 except the 15 nucleotides at the 5’ end” (Cohen, 2020).
This raises the pertinent question as to why Zhengli Shi would claim that she observed
that SARS-COV-2 matched a short RdRp sequence of 4991, then resequenced it de novo, if it
had already been sequenced in 2018. It certainly seems strange not to even mention that she
had already fully sequenced it back in 2018.
Undoubtedly, another pressing question is how BatCov 4991 RdRp and RaTG13 RdRp
can be exactly the same, if they were sequenced with 4 years of difference, yet without any
deterioration or noise, given that the fecal sample allegedly “disintegrated” after being
sequenced (Barclay, 2020).
Because of increasingly vociferous complaints from independent researchers about the
above mentioned discrepancies concerning RatG13 (Colaiacovo, 2020b, Gartland, 2020;
Zhou et al. (2020b) felt compelled to publish an “addendum” to their original paper on 17
November 2020, which claimed that:
“In 2018, as the next-generation sequencing technology and capability in our laboratory
had improved, we performed further sequencing of these bat viruses and obtained almost the
full-length genome sequence (without the 5′ and 3′ ends) of RaTG13. In 2020, we compared
the sequence of SARS-CoV-2 with our unpublished bat coronavirus sequences and found that
it shared a 96.2% identity with RaTG13. RaTG13 has never been isolated or cultured”
(Addendum, 2020b; Zhou et al.).
However, supporting data for these claims was not provided and the addendum itself
seems not to have been peer reviewed. This lack of data and professionalism unfortunately
raises further significant questions about the reliability of Zhou et al.’s (2020) research
(Suryanarayanan, 2020d)
In the earlier Q & A with Science Magazine in July (Cohen, 2020), Zhengli Shi claimed
without any supporting evidence that WIV had secretly tested all staff and students at WIV
for any presence of bat SARSr-CoV or SARS-CoV-2 in their sera samples:
To date, there is zero infection of all staff and students in our institute.” (Cohen, 2020)
Professor Shi also denied that WIV had either carried out or collaborated on any gain-of-
function experiments with coronaviruses that were not published (Cohen, 2020) as claimed
recently by the United States Department of State (2021b), while admitting that her
laboratory still has unpublished data concerning experiments involving the inoculation of
unpublished bat SARS-COV like viruses into hACE2 mice in 2018 and 2019:
We performed in vivo experiments in transgenic (human ACE2 expressing) mice and
civets in 2018 and 2019 in the Institute’s biosafety laboratory. The viruses we used were bat
SARSr-CoV close to SARS-CoV. Operation of this work was undertaken strictly following the
regulations on biosafety management of pathogenic microbes in laboratories in China. The
results suggested that bat SARS-CoV can directly infect civets and can also infect mice with
human ACE2 receptors. Yet it showed low pathogenicity in mice and no pathogenicity in
civets. These data are being sorted and will be published soon” (Cohen, 2020)
5. UNDERSTANDING THE 7896 CLADE
It is important to note that six of the RaTG13 amplicons contain the number “7896” in
the file names, supporting the hypothesis that RaTG13 was indeed an in-silico construct
generated partly with primers based on the unpublished (apart from RdRp) 7896 clade. This
clade’s published RdRps are in fact very similar to RaTG13 and SARS-CoV-2. The
amplicon’s file names in question are as follows (Anon, 2020a) and illustrated in Figure 5
below.
28. SRR11806578.28 SRS6146537 name: RaTG13-R-1-1_7896-1-F1_2017-06-20_E03
29. SRR11806578.29 SRS6146537 name: RaTG13-R-1-1_7896-1-R1_2017-06-20_G03
30. SRR11806578.30 SRS6146537 name: RaTG13-R-2-1_7896-2-F1_2017-06-03_A07
31. SRR11806578.31 SRS6146537 name: RaTG13-R-2-1_7896-2-R1_2017-06-03_A08
32. SRR11806578.32 SRS6146537 name: RaTG13-R-4-1_7896-4-F_2017-06-20_F03
33. SRR11806578.33 SRS6146537 name: RaTG13-R-4-1_7896-4-R_2017-06-20_H03
Figure 5. RaTG13 Amplicon Sequences: Appendix 6 (Francisco A. de Ribera).
Thus, it is surprising that this 7896 clade seems both close to RaTG13 in the
sarbecovirus phylogenetic tree and that the same number, 7896, is used in the file names for
six of the RaTG13 amplicons. Also surprising is the fact that the 7896 sequences were not
named as SARS like viruses, nor were their collection dates and exact locations (China)
published on GenBank or by Latinne et al. (2020) in the paper that referenced them.
The RdRp sequences of the 7896 clade were published in June 2020 as part of a series
of over 600 viruses described by Latinne et al. (2020) from the EcoHealth Alliance and the
sequence data was submitted on 13 August 2019 by the Key Laboratory of Special Pathogens
and Biosafety of the Wuhan Institute of Virology (NCBI, 2020).
No details were given except that they were 8 betacoronaviruses, possibly those
mentioned in the addendum published by Zhou et al. (2020). From the published RdRp
sequence data, we can see that one of the 8 sequences appears to be very near RaTG13 on the
sarbecovirus phylogenetic tree. Unfortunately, further independent analysis has been
hampered by the fact that the data uploaded to GenBank by Latinne et al. (2020) included
duplicate and inconsistent data, as well as several conflicts in the names used (Zhou et al.,
2018), as can be observed here:
https://ncbi.nlm.nih.gov/nuccore/MN312515
https://ncbi.nlm.nih.gov/nuccore/MF769452
To summarise, it is surprising that this 7896 clade was not given more attention by
Latinne et al. (2020) nor by WIV, who apparently decided not to fully sequence the eight
viruses beyond their RdRp, despite one of them being the second or third closest virus to
SARS-CoV-2. It is also surprising that neither the exact location nor date of collection were
published by WIV or Latinne et al. (2020). To add more confusion to understanding this
clade, the RaTG13 amplicon dates which showed 2017 also featured the "7896" label.
Does this mean that 7896 clade was sequenced in 2017, before RaTG13 in 2018?
The paper which described the 7896 clade, Latinne et al. (2020) was initially published as
a pre-print on Biorxiv on May 31, 2020, despite being submitted long before to Nature for
review on October 6 2019. The Fasta files were prepared (supposedly) on 13-Aug-19, and
received by Nature on 06-Oct-19, then processed by NCBI on 07-Nov-19, with an embargo
until 01-Jun-20.
However, it is logical to assume that there must be an initial draft of the paper which
should be made public by EcoHealth alliance. This would allow independent researchers to
analyse the identified discrepancies in order to determine if the WIV cultured any virus from
this clade in animals or cell lines, or used any of the 7896 unpublished sequences as
“backbones” for creating chimeric viruses for experiments in hACE2 mice or ferrets.
Regarding the published accounts of sampling of bat viruses at the Tongguan abandoned
copper mine shaft, Ge et al. (2016) conducted a surveillance of coronaviruses in between
2012 and 2013 which reported 276 bat samples. However, the addendum published in
November 2019 by Zhou et al. (2020b) revealed that another 1046 samples were collected
between 2014 and 2015 including 134 unpublished alphacoronaviruses and 7 unpublished
betacoronaviruses.
So, it is now clear that there were a total of 10 betacoronaviruses discovered at the
abandoned mineshaft, one of them being a non-SARSr and the other 9 SARSr, including
RaTG13 and the eight viruses of 796-clade. "Initially, Ge et al. (2016) stated that only one of
the two reported betacoronaviruses sampled was a “SARS like” virus. However, it has only
recently been revealed that not only betacoronaviruses collected in the Tongguan mineshaft
between 2012 and 2013 were “SARS-like” but also the eight members of the confusing 7896
clade, collected between 2014 and 2015 are in fact also “SARS-like” (Zhou et al., 2020b).
Again, this conflicting data reveals a pattern of obfuscation and lack of transparency
regarding both sampling and publication of viral sequences.
Independent researchers from DRASTIC (Colaiacovo, 2020b, Gartland, 2020) discovered
from an analysis of the 7896 BigD data, that they were collected in Yunnan in May 2015. So
far it has not been clarified if they were collected in the same abandoned copper mineshaft as
RaTG13 and surprisingly, no further information has been forthcoming from either WIV or
EcoHealth Alliance on that question. Professor Shi revealed the names of the 8 viruses of the
7896 clade (highlighted in red in Figure 6) in a lecture on December 3rd, 2020:
Figure 6. Slide from lecture: 7896 Clade (Académie Nationale de Médecine, 2020)
The whole 7896 clade (8 viruses) was also published in a slide in professor Shi’s
ESWI20202 lecture in December 2020 (Figure 7, highlighted in red). This tree was built with
sequences that were larger than the partial RdRp, but not the whole genome:
Figure: 7. ESWI20202 lecture: 7896 Clade (ESW1 TV, 2020)
Two members of the 7896 clade (Ra 7909 and Ra 7924) was also clearly visible in
another slide presented by Professor Shi at the same ESW120202 lecture (ESWI TV, 2020),
referred to as “Mojiang Bat CoVs” (Figure 8) with the title “From SARS to COVID-19,
understanding the interspecies transmission of SARS-related coronaviruses” at the 7th ESWI
Influenza Conference:
Figure 8. Mojiang Bat CoVs (Ra7909 and Ra7924) (ESWI TV, 2020, Timestamp: 14:45)
So, it is now clear, from the December 2020 slide shown by Professor Shi (ESWI TV,
2020) that this 7896 clade did in fact come from the same abandoned mineshaft as RaTG13,
or at least that the range of sample IDs 7909-7924 came from the mineshaft, since the two
viruses mentioned in the slide are referred to as “Mojiang Bat CoVs”.
However, to add yet more confusion to the issue, in a more recent February 21st, 2021
lecture by Professor Shi ”Dangerous Liaisons Workshop - Day 1-Origin & spread of
coronaviruses" (HKU-Pasteur, 2021), the two viruses previously listed in her slides in
December 2020, "Mojiang bat CoVs: Ra7909 and Ra7924” (ESWI TV, 2020), had
mysteriously vanished from the latest slide (Figure 9):
Figure 9: Interspecies Infection. Dangerous Liaisons Workshop (HKU-Pasteur, 2021)
Interestingly, Professor Shi has claimed previously that Bat-SARS-r of clade 1 could
use the hACE2 receptor, albeit with different levels of affinity. Therefore, Ra7909 and
Ra7924 should also enjoy this hACE2 binding ability. Indeed, it is certainly likely that the
complete 7896 clade enjoyed the ability to bind to human ACE2 to varying degrees as was
the case with BtCoV 4991, given the observation by WIV Bat Researchers, Fan et al. (2019)
that “The S protein in certain strains is capable of using human ACE2 as a receptor and thus
poses a direct threat to humans. Interestingly, all the SARSr-CoVs that are capable of using
human ACE2 were found in R. sinicus in Yunnan Province ". R. Affinis was thus discovered
by WIV to be a new host for SARS-r bat CoV with potential to bind to hACE2.
Professor Shi, perhaps inadvertently, revealed these rather disturbing facts in
December 2020, and then removed it from her presentation in February 2021, a fact that the
scientific community was unaware of until recently. In conclusion, it has been shown that
Professor Shi:
Obfuscated about when WIV actually sequenced RaTG13 (2018, not 2020).
Left the 7896-clade (the 2nd closest viruses to SARS-CoV-2 RdRp) embargoed for
months.
Failed to disclose that WIV had in fact sequenced the spike proteins of the 7896-
clade.
6. QUESTIONS CONCERNING RaTG13 AND THE 7896 CLADE
We are left with a series of unanswered questions, some listed by Rahalkar & Bahulikar
(2020A) in their intriguing study “Lethal Pneumonia Cases in Mojiang Miners (2012) and the
Mineshaft Could Provide Important Clues to the Origin of SARS-CoV-2” and others from a
petition to the WHO Investigative Team into the origins of SARS-COV-2 (Ipetitions, 2021),
with the remainder from three lists of questions prepared by the DRASTIC scientific
collective (DRASTIC, 2020a; 2020b; 2020c).
A. RaTG13 FAECAL SAMPLE
1. Why are the Bacteria levels found in the RaTg13 faecal swab unusually low?
2. Were the faecal swab samples of RatG13 in the WIV Lab Freezer discarded few
months ago?
3. Was the RNA or the sample of BtCoV4991 not degraded after 7 years?
4. If, as now known, WIV Researchers were studying RaTG13 in 2018, how can this
fact be compatible with Petr Daszaks’s statements that: “We didn’t do anything about
it and put it in the freezer”?
5. Why is the RaTG13 faecal sample not more available for external examination?
6. Was it possible for the degraded RaTG13 sample to provide a proper “complete
genome” by itself, without the generation of NA sequences produced by passage and
spiked into the sample using viral amplicon products?
B. RaTG13 SEQUENCE DATA
1. The RaTG13 sequence was published, so, why is the chromatogram not available?
2. Did RaTG13 came from a degraded sample dipped in amplicons, enriched in primer
dimers and tandem repeat products randomly ligated together by illumina preparation
process, in an absence of any proper templates?
3. Was RaTG13 a consensus sequence as recently claimed by Peter Daszak in
an interview (TWiV 623) with Vincent Racaniello?
4. The amplicon sequencing data on NCBI clearly shows that the WIV accessed the
RaTG13/4991 sample repeatedly in 2017 and 2018. So, why did Peter Daszak claim
that it was just sitting forgotten in a freezer for 6 years (2013–2020), when the data
clearly shows that they had begun the CoV characterization pipeline for RaTG13 in
2017?
5. Did the Wuhan Institute of Virology team newly extract RNA from the BtCoV4991
physical sample or did they just sequence the stored RNA sample?
6. Was RaTG13 or BatCov 4991 ever applied to Vero E6 (Green Monkey Kidney) cells
to see if more virus particles can be cultured?
7. Was the Spike gene from RaTG13 or BatCov 4991 ever inserted into a closely related
CoV backbone (WIV1) to try to generate virus particles in Vero E6 cells?
8. Did WIV use RaTG13 or BatCov 4991 in an ACE2 cell entry assay to see if the
viruses can enter human cells via ACE2 and replicate?
9. Was RaTG13 characterized after being discovered in 2013?
10. Why does the published RaTG13 amplicon sequence data from WIV contain 40%
unrecognizable random sequences that show no relations to anything on BLAST and
the remainder were mostly Ribosomal RNA?
11. Which laboratories were given a sample of Bat Cov 4991 apart from EcoHealth
Alliance?
12. If you go to the RaTG13 genome accession and to bio-sample where you need to find
all the information about the collected sample, why is only the country name (China)
given, but not the specific location? This is extremely unusual, especially since the
“TG” in RaTG13 designated its specific location.
13. Has anyone apart from WIV tried to amplify BatCov truncated sequence 4991 to
generate a total genome sequence?
14. Why does the mNGS data for RaTG13 contain nearly entirely Repeat sequences and
unrecognizable reads (not resembling anything) with no bacterial reads?
15. Can WIV coherently explain the differences in published sequence data for the
RATg13 faecal swabs?
16. Why did Shi’s 2020 paper not cite the original WIV paper that described their
discovery of RaTG13?
C. QUESTIONS ABOUT THE MOJIANG MINERS PNEUMONIA CASES
1. What kind of samples did the WIV receive from the Mojiang miners?
2. Were all samples stored at WIV?
3. Are these samples available for study by other researchers?
4. Were any viruses isolated and is there any DNA/RNA available from these samples?
5. Was PCR performed on the miners' samples and other available sequences?
6. Which antigen was used for the Ab detection in the pneumonia patients?
7. What was the exact protocol used?
8. Why is this information not available in any of the seroprevalence studies by WIV?
9. Why were the severe pneumonia cases in 2012 not mentioned in any of the WIV
publications before 2020?
10. Were any SARS-like CoV isolated from the bat fecal samples collected in 201213?
11. Why were the Mojiang miners pneumonia cases in 2012 not reported to any public
health agency like the WHO?
12. Why did programs like PREDICT not mention the lethal pneumonia cases as a mini-
outbreak?
13. Was the mineshaft in Mojiang closed, when?
14. Was the mine open for researchers and were any samples collected after 2014?
15. Why was the Mojiang mine being visited by researchers until October 2014?
16. Why did Dr. Shi attribute the outbreak in Mojiang to a fungus in the interview with
Scientific American?
17. Did any of the researchers who visited the Mojiang mineshaft get infected by any
coronavirus between 2012 and 2019?
18. Are there any whole genome sequences available for SARS-like CoV originating
from this mine?
19. Why is the viral pathogen database associated with the project (2013FY113500) not
accessible anymore?
20. Does WIV (or anyone else) still have blood or sputum samples of the 4 miners who
tested positive for SARS antibodies in 2012? Can we retest those?
21. Why wasn’t miners’ pneumonia or positive SARS ab status mentioned in WIV
papers?
22. Did WIV sample bat guano at the TG Mine location in Yunnan, is this a common
practice?
23. Can WIV clarify the full details of the 2012 pneumonia outbreak among the Mojiang
miners, especially regarding the subsequent samplings and all blood and BALF
results?
24. Can WIV clarify what happened to the samples collected from the Mojiang miners
between 2012 and 2019 and whether they are still available for independent analysis?
25. Did WIV culture any virus from the Tongguan mineshaft pneumonia cases in animals
or cell lines? If so, were the sequences used as “backbones” for creating other
viruses?
26. Was the 2012 Yunnan (TG) mine outbreak declared to the WHO?
27. What is the current condition of miners who survived the pneumonia outbreak at
Tongguan mineshaft in 2013? B. Where are they now? C. What exactly do they have
antibodies for? D. Have they had recent T-Cell studies? E. Are they available to speak
to?
28. Do any other institutes in Wuhan, not only WIV, have samples from Mojiang Yunnan
mineshaft?
29. If the Mojiang pneumonia cases were known to Zhong Nanshan, Zhengli Shi, George
Gao Fu (Now Head of CCDC) and Qin Jin of IPB (Beijing), why did none of them,
report it to the WHO or discuss it in their subsequently published papers?
30. Why was the reference to a SARS CoV being a cause of the Mojiang pneumonia
outbreak in 2012 never mentioned in English Language Papers, News Reports or
EcoHealth Alliance reports, and only mentioned in the Chinese thesis?
D. QUESTIONS ABOUT THE 7896 CLADE
1. Some RaTG13 amplicons include a "7896" label. So, was Ra7896 in fact used for
sequencing RaTG13?
2. Why did WIV not fully sequence the 8 SARSr of the 7896-clade further than their
RdRp when they were the second closest viruses to SARS-CoV-2?
3. Were these 8 remaining SARSr from the 7896 clade collected from the same
Tongguan mine as RaTG13?
4. Will EcoHealth publish the initial draft of Latinne et al. (2020)?
5. Peter Daszak facilitated a large upload of viral genome sequences to GenBank
recently for IDs ranging 6233 to 9408 (2014–2015). Why has he not facilitated the
uploading of previous missing IDs, from 2012 to 2013?
E. OTHER RELATED QUESTIONS.
1. What is the precise motivation behind the WIV taking databases associated with the
program that identified RaTG13 offline and deleting traces of them?
2. There is a correlative series of isolates from WIV but two are missing from the series.
Specifically, why were the WIV6 and WIV15 isolates never disclosed?
3. Was Peter Daszak somehow involved in the Tongguan bat virus sampling expedition?
4. Will WIV and Peter Daszak go on the record to deny that WIV Scientists were
studying BatCov/4991 and other as yet unpublished virus samples from Mojiang
between 2013 and 2019?
5. Why did WIV Bat research team not upload viral sequences from rodents and shrews
from Yunnan? (Only Bat Researchers, Jin and Huang, declared that they had collected
samples from them in Tongguan, although it was a normal practice in other locations
(e.g. Fugong)
6. How is it possible that the pandemic prevention workflow for discovering a novel
SARS virus in a cave where miners got ill with a SARS-like pneumonia was to throw
the virus in a freezer until a pandemic from a closely related virus breaks out?
7. Why has the exact, detailed list of all WIV samples, isolates, etc. as well as the
Wuhan University and the Hubei CDC samples and isolates not been shared with the
WHO or other countries?
7. CONCLUSION
In light of the questions, criticisms and anomalies presented in this brief report, which
reveal a clear pattern of obfuscation and lack of transparency concerning the provenance of
RaTG13, as well as its sequence data, the publications referencing it and anomalous updates,
especially with regard to the amplicon sequences, the authors urgently call for a full
independent investigation to be carried out forthwith. The authors also call on the Wuhan
Institute of Virology to immediately share all their data on the 7896 clade and for EcoHealth
Alliance to cooperate fully with any investigation into related sequences and databases. This
is especially important since the study identifying RaTG13 was partially supported by a
USNIAID grant: R01AI110964 (Ge et al., 2016), meaning that US taxpayers' money was
used for collecting and studying coronavirus samples by the Wuhan Institute of Virology.
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