The Seeker’s work is both broad and detailed with very specific links to the datasphere sign of COVID origin that are well in advance of virologists in this field.
There are many bioinformatics based epistemologists and interdisciplinary researchers that while they do not have a faculty home and often remain anonymous or censored to the point of almost being non existent …these emerging areas are leading GOF ethics and COVID origin forensics analysis.
Not Virology.
Virology has failed.
It has failed as there is an essential error in application and approach here in Dual Use Research of Concern studies and biosynthetics technologies …this is simply not the safe realm of fair weather thinking. DURC, even before GOF studies, are always prosperous and flourishing on the one hand and always open to Biological and Informational Warfare on the other.
This means the details count…many details that The Seeker has worked over many years to uncover…and many more that demonstrate the idea that science and politics are distinct forms of thinking is weak…human thought deals with details well in some cases and appallingly in others.
Below is an email chain that has examined simply one aspect of COVID Origin that has finally made its way to the relevant Defence Minister’s office in Australia.
You will notice that the bioinformatics herein applied forensically are simply beyond the scope of the virologists involved and even though they use the term <<Trust but Verify >> and attempt to apply this methodology they fail.
Subject: RE: Case CAS-1438068-G6V5R2- National Library of Medicine Customer Service confirmation TRACKING:000435001455525
Dear NLM GenBank Indexers,
Please pass on the relevant details to me here on my University of Notre Dame Australia student email account, and also on to Hon Perrett, Graham (MP) graham.perrett.mp@aph.gov.au
so the relevant Australian Federal Ministers can have access to this relatively hidden information once the files have their suppression lifted and the missing and overwritten files can be accounted for and also this data can be then passed on to the relevant Australian government departments for analysis.
I am not sure of the members of parliament for Prof Holmes and Prof Mary Collins and for University of Sydney…but they can send the details on to their local representatives in parliament once the details are provided.
Subject: Case CAS-1438068-G6V5R2- National Library of Medicine Customer Service confirmation TRACKING:000435001455525
Thank you for contacting the U.S. National Library of Medicine (NLM). The details of your message are listed below. You can expect to hear from us within 2 to 5 business days. For additional information about NLM products and services, please visit https://support.nlm.nih.gov.
Case Information:
Case #: CAS-1438068-G6V5R2
Summary: [EXTERNAL] Data disclosures in COVID Origin from University of Sydney and WIV
Details:
Hon Graham Perrett,
MP for Moreton
Dear Graham,
My name is Tommy Cleary and I am a resident of your Federal Electorate and a postgraduate student at University of Notre Dame Australia, and a post graduate researcher examining COVID origin with interdisciplinary methods from epidemiology to epistemics.
Below are the emails I mentioned earlier to Prof Edward Holmes of University of Sydney and Prof Zhengli Shi of the Wuhan Institute of Virology …and with CCed to their research and publication collaborators and critics that should be able to help with the details required by the Defence Minister and other relevant Ministers of the Australian Federal Parliament.
Unfortunately preliminary investigations confirm what was suspected; the recovered data from GenBank thus far already demonstrate serious signs of epistemic themes consistent with gain of function experiments and investigations targeting cell apoptosis in TCell populations, and elsewhere serious signs of reverse genetics with amino acid identity >99% for <<ZXC21 and ZC45>> in this dataset recovered so far, where both these issues need to be attended to in the context of ongoing information domain activity and suspected biological warfare programs, if not in WIV then in nearby PLA run laboratories.
<<Trust but Verify>> methodology cited by Holmes means these issues need to be refuted with further evidence and not simply overtly denied while evidence that can counter these claims continues to be withheld.
What I mean by this is that there are serious concerns here that these sequences found in GenBank, and perhaps more that have been deleted from GenBank, have been deliberately withheld from before the time of discovery of early COVID pandemic outbreak in December 2019 with details missing since October 2019, with or without the knowledge of Prof Edward Holmes and even perhaps without even the knowledge of Prof Zhengli Shi. But someone did know, and seeking these questions and the relevant data sets have been seriously important since the time of outbreak and I apologise that it has taken so long. I am a volunteer interdisciplinary researcher with limited means and that these data sets and the other deleted and overwritten data sets are obvious to me means that many, many, others would surely be aware of these issues and either stayed silent or worse, silenced others.
Please send any questions, that you or the relevant Ministers may have, on and please do not delay in asking the relevant Ministers and their departments for their assistance… and please do not ask me to read more books in the local State Library …or send the request on to the Health Ministers involved as they have expressed zero interest or understanding of the implications of this hidden data from WIV and University of Sydney in the past.
Now that these data sets have been partially recovered from GenBank it is time to inform the relevant Australian Ministers via your local Member of Parliament of their implications…when you learnt of their contents…what your understanding of this data set is and why it has been hidden for so long…etc.
Remember that these areas of Virology are ALWAYS considered Dual Use Research of Concern.
This means that one of their applications is prosperous and welcome.
And the other is not, the other use of dangerous virology is linked to biological warfare and information warfare.
Both of these considerations must be front of mind in all dealings with such data sets.
I do not know why you appear to be only capable of fair-weather thinking, but it is illogical and intolerable.
Missing data is this field of concern is a serious matter.
Data availability saves lives even if that data is sensitive and the ontological issues that Bioweapons data sets involve are potentially catastrophic.
Please be more forthcoming with the data sets herein and their linked relevant preprint papers.
Conversations that concern all our cells, and their internal language of RNA so important to virology, are not epistemically containable within intellectual property jurisdictions arbitrarily asserted nor should these details be perpetually held in secrecy especially in the midst of a pandemic that has killed millions and will kill millions more people…these paragraphs of RNA are also our shared biological and dignified heritage as human beings on our one living planet…from now on and until this virus is eliminated from circulation it is part of our shared experience of civilisation even to those who have not been born into existence and yet still may need to live in a world where this virus thrives because secrets have to date prevailed over open discussion.
Thank you for your help with these questions of concern.
From earlier email and below email to Prof ZLShi of WIV:
Some of the most difficult aspects of COVID Origin research have been the various aspects of epistemic crisis induced by patchy availability to relevant data sets.
The <<Politics v Science>> complaint is tired and old…as you know current research based on recovered data sets are more focused on <<Trust but Verify>> methodology.
This is the methodology of biological warfare and information domain warfare investigations.
One such data set is related to a WIV paper that Drosten reviewed in the past…BC…Before COVID.
Hu B, Zeng L-P, Yang X-L, Ge X-Y, Zhang
W, Li B, et al. (2017)
<<Discovery of a rich gene pool
of bat SARS-related coronaviruses provides new
insights into the origin of SARS coronavirus.>>
PLoS
Pathog 13(11): e1006698
As you know important issues such as apoptosis are investigated in some detail and with such a potent aspect of <<Dual Use Research of Concern>> being investigated I do agree that <<Trust but Verify>> Methodology is important:
<<Induction of apoptosis by the ORF8a of the newly identified bat SARSr-CoV:
We conducted transient transfection to examine whether the ORF8a of SARSr-CoV Rs4084
triggered apoptosis. As shown in Fig 9B, 11.76% and 9.40% of the 293T cells transfected with
the SARSr-CoV Rs4084-ORF8a and SARS-CoV Tor2-ORF8a expression plasmid underwent
apoptosis, respectively.
In contrast, transfection with the empty vector resulted in apoptosis in
only 2.79% of the cells.
The results indicate that Rs4084 ORF8a has an apoptosis induction
There was a subsequent data set uploaded to GenBank that has not been made fully available yet: <<Yu218PrePrint>> with 163 submissions largely suppressed by GenBank Indexers.
As one of the authors of this PrePrint is you, Prof Edward C Holmes of University of Sydney, and you attempted <<Trust but Verify>> methodology in a Twitter thread before the COVID Select Committee discussions of related material.
In any case the data in GenBank has been largely recovered,
With both ends of this 163 GI slot data set soft and showing signs of deleted and overwritten files that you and your coauthors appear to have submitted and then had deleted;
With only 31 GI slots deleted on <<13-OCT-2019>> at the earlier ORF8 end of the data set that should be available soon with the institutional changes in the US.
Which interestingly frames the timestamps and GI/ACCESSION number series at <<Oct 30, 2019 08:15 PM>>
With another data deletion and replacement event?
Here 74 GIs are suspected of being deleted and replaced.
<<Trust but Verify>>
Thus, preliminary data analysis demonstrates that <<Yu2018PrePrint>> must have ALL associate datapoints, published and unpublished, suppressed and deleted, handed over to the scientific and related academic communities for detailed examination…and so I am writing to you again.
The part that is most important for you is the set of earliest submissions that holds bioinformatics signs that reflect the same methodology displayed in the paper <<Hu2017>>
That is even at this early stage:
Isolated ORF8a proteins have important links to earlier
Apoptosis studies published.
Apoptosis as in viruses that trigger cells to die.
Besides <<Apoptosis>> there are other aspects of this data set that imply reverse genetics systems use and other synthetic biology means linked to
<<ZXC21 and ZC45>> need to be thoroughly investigated and excluded via <<Trust but Verify>> methodology.
Also, there are species data that mean potential <<RaTG13/Ra4991>> host species remains ambiguous and certain issues must be excluded eventually...
among other important preliminary findings.
These are the job of epidemiologists and epistemologists involved with the bioinformatics analysis of COVID Origin and related Biological and Information Warfare investigations.
Where the taxonomy for raw data loaded by Prof ZL Shi cites <<RaTG13/Ra4991>> as
<<Rhinolophus ferrumequinum: 10.66%>> instead of <<R. affinis>> has again attracted verification level scrutiny of this whole data set and related papers.
The idea that not addressing these inconsistencies will simply make them go away is ridiculous and if you cannot gather the resources yourself to attend immediately to these ongoing concerns then please allow the University of Syndey to provide the necessary resources to explain where this data can be disclosed.
Again, Prof Mary Collins should be able to help.
I would like the <<WIV and University of Sydney>> researchers that have sent this important data to GenBank to have a chance to frame and explain the data set as much as possible in the context of a related paper and peer reviewed publication.
The paper <<Discovery of a rich gene pool of bat SARS- related coronaviruses provides new insights into the origin of SARS coronavirus>> represents a unique publication opportunity for this data set and I have thus forwarded my analysis thus far to Prof Drosten and some others CCed here...and I look forward to you finally addressing these issues of concern without whingeing about Science v Politics which is a false and convenient dichotomy.
Remember Edward, you have raised the concept of << Trust but Verify, Доверяй, но проверяй>> which quite simply has a requirement in disclosure much higher than you have even attempted in your multiple publications since <<13-OCT-2019>>
Are you asking your readers to believe that you are really so stupid as to misplace 163 GI slots of data and simply forget about the potentially overwritten 31 GI slots on one end of this suppressed data set as well as 74 GI slots that are suspect on the other end of this data set?
A claim to such stupidity is equally dangerous as the banality in the alternative.
From your previous email dated 11 Feb 2021 you state:
<< Personally, I have no problem with people being anti-gain-of-function and I’m a bit agnostic myself.
However, this blinded them to think that SARS-CoV-2 came from the WIV for which there is no evidence.
I’m not angry with this position.
What I do object to is people claiming that some of the key data was fabricated.
I’m involved in some of these papers and it is just insulting and evil nonsense..>>
Grow up Edward and open your eyes to the implications of your own data sets.
Get some help and find a way to make this data available for more in-depth analysis with the tools available on GenBank that can easily demonstrate the risk of systemic reverse genetics was high with links to <<ZXC21 and ZC45>>
With >99% Spike Protein identity for <<ZC45>> in the consecutive GI in this data set <<GI 1769824578 to 1769824584>> as a taste of the type of analysis that needs to be completed from a forensic bioinformatics approach appropriate to this <<Trust but Verify>> theme of COVID Origin that you have raised:
With an Addendum or Erratum or some other academic publication mechanism from you Prof Edward Holmes the WIV data sets that have been submitted to GenBank may be able to be published as a supplement somewhere and the GenBank suppressions lifted so that a complete analysis can be performed?
The details of how this may happen with the tools available to <<PLoS Pathogen>> editors or other academic publication resources that you may have available are at your discretion…
Would you instead require a formal <<letter to the editor>> in correspondence from me or other COVID Origin researchers addressed to one of the editors of the many linked publications to your COVID Origin work?
Looking forward to your input and reading any resultant publication and or disclosures with anticipation.
Note in the email below that Prof Zhengli Shi indicates that all the relevant data is in GenBank: << You can find our publications and sequence information in the GenBank and do your own analysis to satisfy your own curiosity.>>
<< Trust but Verify>> is not simple curiosity.
It essentially asks, can we survive ourselves.
Not maliciously, but honestly and openly:
Can we survive our own shared epistemic path that seeks prosperity but faces the challenge of resultant civilisation ending weaponry?
Kind regards
Mr Tommy Cleary
Postgraduate Student UNDA.
Across the road from University of Sydney, Australia.
Subject: Re: RE: Missing DOI “Wildlife-borne Viral Pathogen Database” Shi Zhengli of the Wuhan Institute of Virology
Dear Mr.Tommy Cleary,
Thank you for your interesting in our database.
For answering your curiosity:
1. The idea of constructing a bat virus database in my lab just began 3 years ago. We have only entered a limit data in this database and the access to the visitors is limited and granted with permission considering the knowledge property. During COVID-19 pandemic, our Institute web server has been fiercely attacked (still going on sometime) and out Institute decided to close down some web pages and databases including the our bat virus database. I'v no idea when it will be open.
2. We have studied bat viruses for more than 15 years. All our work regarding the different type of bat coronavirus (partial sequences or full-length genome sequences) have been published and the sequence and sample information have been submitted to GenBank. You can find our publications and sequence information by your own and do your own analysis to satisfying your curiosity. But I would like to remind you to ask the help from a coronavirologist in avoiding of misunderstanding what we have done.
3. During 15 years, we only isolated 3 bat coronaviruses (virus can grow in cell culture in the lab) and all of them has been published in the international journals. The other bat coronaviruses are known from their genomic sequences. Again, I would like to remind you to ask a virologist to help you to understand the difference between a live virus and a genomic sequence.
4. I don't understand why there are some people in this world lost trust to sciences and scientists. The sciences need prove but the conspiracy don't because no one can prove a conspiracy.
5. I'll not answer any of your questions if your curiosity is based on the conspiracy of "man made or lab leak of SARS-CoV-2" or some non-sense questions based on your suspicion. No trust, no conversation.
“Bat Severe Acute Respiratory Syndrome-Like Coronavirus WIV1 Encodes an Extra Accessory Protein, ORFX, Involved in Modulation of the Host Immune Response”
This type of paper shows this data base of SARS-like Coronavirus from bats holds information about the origins of the current COVID19 pandemic and the way features of the codes of these CoV viruses can help understand the type of medicine needed to help people survive when infected.
Any information that you can give, however mundane, can help save lives and reduce suffering of this current pandemic.
Even taking the time to explain the limits (legal or otherwise) of what you can provide about DOI numbers is helpful.
Very good Simon.
The Seeker’s work is both broad and detailed with very specific links to the datasphere sign of COVID origin that are well in advance of virologists in this field.
There are many bioinformatics based epistemologists and interdisciplinary researchers that while they do not have a faculty home and often remain anonymous or censored to the point of almost being non existent …these emerging areas are leading GOF ethics and COVID origin forensics analysis.
Not Virology.
Virology has failed.
It has failed as there is an essential error in application and approach here in Dual Use Research of Concern studies and biosynthetics technologies …this is simply not the safe realm of fair weather thinking. DURC, even before GOF studies, are always prosperous and flourishing on the one hand and always open to Biological and Informational Warfare on the other.
This means the details count…many details that The Seeker has worked over many years to uncover…and many more that demonstrate the idea that science and politics are distinct forms of thinking is weak…human thought deals with details well in some cases and appallingly in others.
Below is an email chain that has examined simply one aspect of COVID Origin that has finally made its way to the relevant Defence Minister’s office in Australia.
You will notice that the bioinformatics herein applied forensically are simply beyond the scope of the virologists involved and even though they use the term <<Trust but Verify >> and attempt to apply this methodology they fail.
Subject: RE: Case CAS-1438068-G6V5R2- National Library of Medicine Customer Service confirmation TRACKING:000435001455525
Dear NLM GenBank Indexers,
Please pass on the relevant details to me here on my University of Notre Dame Australia student email account, and also on to Hon Perrett, Graham (MP) graham.perrett.mp@aph.gov.au
so the relevant Australian Federal Ministers can have access to this relatively hidden information once the files have their suppression lifted and the missing and overwritten files can be accounted for and also this data can be then passed on to the relevant Australian government departments for analysis.
I am not sure of the members of parliament for Prof Holmes and Prof Mary Collins and for University of Sydney…but they can send the details on to their local representatives in parliament once the details are provided.
Thank you for your help.
Kind regards
Tommy Cleary
From: NLM Support <nlm-support@nlm.nih.gov>
Sent: Tuesday, February 18, 2025 10:44 PM
To: Tommy Cleary <tommy.cleary1@my.nd.edu.au>
Subject: Case CAS-1438068-G6V5R2- National Library of Medicine Customer Service confirmation TRACKING:000435001455525
Thank you for contacting the U.S. National Library of Medicine (NLM). The details of your message are listed below. You can expect to hear from us within 2 to 5 business days. For additional information about NLM products and services, please visit https://support.nlm.nih.gov.
Case Information:
Case #: CAS-1438068-G6V5R2
Summary: [EXTERNAL] Data disclosures in COVID Origin from University of Sydney and WIV
Details:
Hon Graham Perrett,
MP for Moreton
Dear Graham,
My name is Tommy Cleary and I am a resident of your Federal Electorate and a postgraduate student at University of Notre Dame Australia, and a post graduate researcher examining COVID origin with interdisciplinary methods from epidemiology to epistemics.
Below are the emails I mentioned earlier to Prof Edward Holmes of University of Sydney and Prof Zhengli Shi of the Wuhan Institute of Virology …and with CCed to their research and publication collaborators and critics that should be able to help with the details required by the Defence Minister and other relevant Ministers of the Australian Federal Parliament.
Unfortunately preliminary investigations confirm what was suspected; the recovered data from GenBank thus far already demonstrate serious signs of epistemic themes consistent with gain of function experiments and investigations targeting cell apoptosis in TCell populations, and elsewhere serious signs of reverse genetics with amino acid identity >99% for <<ZXC21 and ZC45>> in this dataset recovered so far, where both these issues need to be attended to in the context of ongoing information domain activity and suspected biological warfare programs, if not in WIV then in nearby PLA run laboratories.
<<Trust but Verify>> methodology cited by Holmes means these issues need to be refuted with further evidence and not simply overtly denied while evidence that can counter these claims continues to be withheld.
What I mean by this is that there are serious concerns here that these sequences found in GenBank, and perhaps more that have been deleted from GenBank, have been deliberately withheld from before the time of discovery of early COVID pandemic outbreak in December 2019 with details missing since October 2019, with or without the knowledge of Prof Edward Holmes and even perhaps without even the knowledge of Prof Zhengli Shi. But someone did know, and seeking these questions and the relevant data sets have been seriously important since the time of outbreak and I apologise that it has taken so long. I am a volunteer interdisciplinary researcher with limited means and that these data sets and the other deleted and overwritten data sets are obvious to me means that many, many, others would surely be aware of these issues and either stayed silent or worse, silenced others.
Please send any questions, that you or the relevant Ministers may have, on and please do not delay in asking the relevant Ministers and their departments for their assistance… and please do not ask me to read more books in the local State Library …or send the request on to the Health Ministers involved as they have expressed zero interest or understanding of the implications of this hidden data from WIV and University of Sydney in the past.
Kind regards
Tommy Cleary.
Dear Edward,
Now that these data sets have been partially recovered from GenBank it is time to inform the relevant Australian Ministers via your local Member of Parliament of their implications…when you learnt of their contents…what your understanding of this data set is and why it has been hidden for so long…etc.
Remember that these areas of Virology are ALWAYS considered Dual Use Research of Concern.
This means that one of their applications is prosperous and welcome.
And the other is not, the other use of dangerous virology is linked to biological warfare and information warfare.
Both of these considerations must be front of mind in all dealings with such data sets.
I do not know why you appear to be only capable of fair-weather thinking, but it is illogical and intolerable.
Missing data is this field of concern is a serious matter.
Data availability saves lives even if that data is sensitive and the ontological issues that Bioweapons data sets involve are potentially catastrophic.
Please be more forthcoming with the data sets herein and their linked relevant preprint papers.
Conversations that concern all our cells, and their internal language of RNA so important to virology, are not epistemically containable within intellectual property jurisdictions arbitrarily asserted nor should these details be perpetually held in secrecy especially in the midst of a pandemic that has killed millions and will kill millions more people…these paragraphs of RNA are also our shared biological and dignified heritage as human beings on our one living planet…from now on and until this virus is eliminated from circulation it is part of our shared experience of civilisation even to those who have not been born into existence and yet still may need to live in a world where this virus thrives because secrets have to date prevailed over open discussion.
Thank you for your help with these questions of concern.
From earlier email and below email to Prof ZLShi of WIV:
Some of the most difficult aspects of COVID Origin research have been the various aspects of epistemic crisis induced by patchy availability to relevant data sets.
The <<Politics v Science>> complaint is tired and old…as you know current research based on recovered data sets are more focused on <<Trust but Verify>> methodology.
This is the methodology of biological warfare and information domain warfare investigations.
One such data set is related to a WIV paper that Drosten reviewed in the past…BC…Before COVID.
Hu B, Zeng L-P, Yang X-L, Ge X-Y, Zhang
W, Li B, et al. (2017)
<<Discovery of a rich gene pool
of bat SARS-related coronaviruses provides new
insights into the origin of SARS coronavirus.>>
PLoS
Pathog 13(11): e1006698
As you know important issues such as apoptosis are investigated in some detail and with such a potent aspect of <<Dual Use Research of Concern>> being investigated I do agree that <<Trust but Verify>> Methodology is important:
<<Induction of apoptosis by the ORF8a of the newly identified bat SARSr-CoV:
We conducted transient transfection to examine whether the ORF8a of SARSr-CoV Rs4084
triggered apoptosis. As shown in Fig 9B, 11.76% and 9.40% of the 293T cells transfected with
the SARSr-CoV Rs4084-ORF8a and SARS-CoV Tor2-ORF8a expression plasmid underwent
apoptosis, respectively.
In contrast, transfection with the empty vector resulted in apoptosis in
only 2.79% of the cells.
The results indicate that Rs4084 ORF8a has an apoptosis induction
activity similar to that of SARS-CoV>>
https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1006698&type=printable
There was a subsequent data set uploaded to GenBank that has not been made fully available yet: <<Yu218PrePrint>> with 163 submissions largely suppressed by GenBank Indexers.
https://web.archive.org/web/20220809085043/https:/www.ncbi.nlm.nih.gov/nuccore/?term=Spread+and+Geographic+Structure+of+SARS-related+Coronaviruses+in+++++++++++++Bats+and+the+Origin+of+Human+SARS+Coronavirus
As one of the authors of this PrePrint is you, Prof Edward C Holmes of University of Sydney, and you attempted <<Trust but Verify>> methodology in a Twitter thread before the COVID Select Committee discussions of related material.
https://web.archive.org/web/20230308013429/https://twitter.com/EdwardCHolmes
In any case the data in GenBank has been largely recovered,
With both ends of this 163 GI slot data set soft and showing signs of deleted and overwritten files that you and your coauthors appear to have submitted and then had deleted;
With only 31 GI slots deleted on <<13-OCT-2019>> at the earlier ORF8 end of the data set that should be available soon with the institutional changes in the US.
From <<GI 1430929924>>
https://ncbi.nlm.nih.gov/protein/1430929924?report=girevhist
to
<<GI 1430929935>>
https://ncbi.nlm.nih.gov/protein/1430929935?report=girevhist
Also, with the Spike end of the data set in GenBank there are signs of potentially deleted files. You see it ends at
<<Rs_161465_Guangdong>> With <<GI 1769824623>>
https://ncbi.nlm.nih.gov/protein/1769824623?report=girevhist
But the ACCESSION numbers and GI and time stamps there after do not correspond correctly!
So from <<GI 1769824625>>
https://ncbi.nlm.nih.gov/protein/1769824625?report=girevhist
To at least
<<GI 1769824699>>
https://ncbi.nlm.nih.gov/protein/1769824993?report=girevhist
Which interestingly frames the timestamps and GI/ACCESSION number series at <<Oct 30, 2019 08:15 PM>>
With another data deletion and replacement event?
Here 74 GIs are suspected of being deleted and replaced.
<<Trust but Verify>>
Thus, preliminary data analysis demonstrates that <<Yu2018PrePrint>> must have ALL associate datapoints, published and unpublished, suppressed and deleted, handed over to the scientific and related academic communities for detailed examination…and so I am writing to you again.
The part that is most important for you is the set of earliest submissions that holds bioinformatics signs that reflect the same methodology displayed in the paper <<Hu2017>>
That is even at this early stage:
Isolated ORF8a proteins have important links to earlier
Apoptosis studies published.
Apoptosis as in viruses that trigger cells to die.
https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1006698&type=printable
This early <<Yu2018PrePrint>> GenBank data set is framed by data linked to <<18-Jul-2018>> GenBank submission time stamps...
and has a bioinformatic structure that implies earlier WIV apoptosis studies with examination of SARS1 like <<ORF8a>> proteins have been continued...
and in the context of COVID outbreak this data and related text needs to be examined in detail.
1) <<Rspp7896_Yunnan ORF8abc MH615800.1
GI: 1430929737>>
https://ncbi.nlm.nih.gov/protein/1430929737?report=girevhist
2)<<Rspp7905_Yunnan ORF8abc MH615801.1
GI: 1430929788>>
https://ncbi.nlm.nih.gov/protein/1430929788?report=girevhist
3) <<Rspp7907_Yunnan ORF8abc MH615802.1
GI: 1430929792>>
https://ncbi.nlm.nih.gov/protein/1430929792?report=girevhist
4) <<Ra7909_Yunnan ORF8abc MH615803.1
GI: 1430929816>> also known as RaTG15
https://ncbi.nlm.nih.gov/protein/1430929816?report=girevhist
5) <<Rspp7921_Yunnan ORF8abc MH615804.1
GI: 1430929896>>
https://ncbi.nlm.nih.gov/protein/1430929896?report=girevhist
6) <<Rspp7924_Yunnan ORF8abc MH615805.1
GI: 1430929909>>
https://ncbi.nlm.nih.gov/protein/1430929909?report=girevhist
7) << Rspp7931_Yunnan ORF8abc MH615806.1
GI: 1430929913>>
https://ncbi.nlm.nih.gov/protein/1430929913?report=girevhist
8) <<Rspp7952_Yunnan ORF8abc MH615807.1
GI: 1430929917>>
https://ncbi.nlm.nih.gov/protein/1430929917?report=girevhist
9) <<Rs151334_Guizhou ORF8ab MH615808.1
GI 1430929921>>
https://ncbi.nlm.nih.gov/protein/1430929921?report=girevhist
ORF8a)
https://ncbi.nlm.nih.gov/protein/1430929922?report=girevhist
ORF8b)
https://ncbi.nlm.nih.gov/protein/1430929923?report=girevhist
Note <<Rs151334_Guizhou ORF8ab>> has only ORF8a and ORF8b without any ORF8c
Followed by an uninterrupted series of GI slots that have been deleted and overwritten by unrelated data,
where the original data needs to be recovered from GenBank.
from
GI 1430929924
https://ncbi.nlm.nih.gov/protein/1430929924?report=girevhist
to
GI 1430929935
https://ncbi.nlm.nih.gov/protein/1430929935?report=girevhist
Besides <<Apoptosis>> there are other aspects of this data set that imply reverse genetics systems use and other synthetic biology means linked to
<<ZXC21 and ZC45>> need to be thoroughly investigated and excluded via <<Trust but Verify>> methodology.
Also, there are species data that mean potential <<RaTG13/Ra4991>> host species remains ambiguous and certain issues must be excluded eventually...
among other important preliminary findings.
These are the job of epidemiologists and epistemologists involved with the bioinformatics analysis of COVID Origin and related Biological and Information Warfare investigations.
Where the taxonomy for raw data loaded by Prof ZL Shi cites <<RaTG13/Ra4991>> as
<<Rhinolophus ferrumequinum: 10.66%>> instead of <<R. affinis>> has again attracted verification level scrutiny of this whole data set and related papers.
https://ngdc.cncb.ac.cn/gsa/taxonomyAnalysis/CRA002424/CRR122287
The idea that not addressing these inconsistencies will simply make them go away is ridiculous and if you cannot gather the resources yourself to attend immediately to these ongoing concerns then please allow the University of Syndey to provide the necessary resources to explain where this data can be disclosed.
Again, Prof Mary Collins should be able to help.
I would like the <<WIV and University of Sydney>> researchers that have sent this important data to GenBank to have a chance to frame and explain the data set as much as possible in the context of a related paper and peer reviewed publication.
The paper <<Discovery of a rich gene pool of bat SARS- related coronaviruses provides new insights into the origin of SARS coronavirus>> represents a unique publication opportunity for this data set and I have thus forwarded my analysis thus far to Prof Drosten and some others CCed here...and I look forward to you finally addressing these issues of concern without whingeing about Science v Politics which is a false and convenient dichotomy.
Remember Edward, you have raised the concept of << Trust but Verify, Доверяй, но проверяй>> which quite simply has a requirement in disclosure much higher than you have even attempted in your multiple publications since <<13-OCT-2019>>
Are you asking your readers to believe that you are really so stupid as to misplace 163 GI slots of data and simply forget about the potentially overwritten 31 GI slots on one end of this suppressed data set as well as 74 GI slots that are suspect on the other end of this data set?
A claim to such stupidity is equally dangerous as the banality in the alternative.
From your previous email dated 11 Feb 2021 you state:
<< Personally, I have no problem with people being anti-gain-of-function and I’m a bit agnostic myself.
However, this blinded them to think that SARS-CoV-2 came from the WIV for which there is no evidence.
I’m not angry with this position.
What I do object to is people claiming that some of the key data was fabricated.
I’m involved in some of these papers and it is just insulting and evil nonsense..>>
Grow up Edward and open your eyes to the implications of your own data sets.
Get some help and find a way to make this data available for more in-depth analysis with the tools available on GenBank that can easily demonstrate the risk of systemic reverse genetics was high with links to <<ZXC21 and ZC45>>
With >99% Spike Protein identity for <<ZC45>> in the consecutive GI in this data set <<GI 1769824578 to 1769824584>> as a taste of the type of analysis that needs to be completed from a forensic bioinformatics approach appropriate to this <<Trust but Verify>> theme of COVID Origin that you have raised:
Rs8561_Guangdong
https://www.ncbi.nlm.nih.gov/nuccore/MH615970.1?report=genbank
to
Rs141567_Guangxi
https://www.ncbi.nlm.nih.gov/nuccore/MH615973.1?report=genbank
See the blast here:
https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=UZK25WJG114
archived here:
https://archive.md/lmEgt
With an Addendum or Erratum or some other academic publication mechanism from you Prof Edward Holmes the WIV data sets that have been submitted to GenBank may be able to be published as a supplement somewhere and the GenBank suppressions lifted so that a complete analysis can be performed?
The details of how this may happen with the tools available to <<PLoS Pathogen>> editors or other academic publication resources that you may have available are at your discretion…
Would you instead require a formal <<letter to the editor>> in correspondence from me or other COVID Origin researchers addressed to one of the editors of the many linked publications to your COVID Origin work?
Looking forward to your input and reading any resultant publication and or disclosures with anticipation.
Note in the email below that Prof Zhengli Shi indicates that all the relevant data is in GenBank: << You can find our publications and sequence information in the GenBank and do your own analysis to satisfy your own curiosity.>>
<< Trust but Verify>> is not simple curiosity.
It essentially asks, can we survive ourselves.
Not maliciously, but honestly and openly:
Can we survive our own shared epistemic path that seeks prosperity but faces the challenge of resultant civilisation ending weaponry?
Kind regards
Mr Tommy Cleary
Postgraduate Student UNDA.
Across the road from University of Sydney, Australia.
Subject: Re: RE: Missing DOI “Wildlife-borne Viral Pathogen Database” Shi Zhengli of the Wuhan Institute of Virology
Dear Mr.Tommy Cleary,
Thank you for your interesting in our database.
For answering your curiosity:
1. The idea of constructing a bat virus database in my lab just began 3 years ago. We have only entered a limit data in this database and the access to the visitors is limited and granted with permission considering the knowledge property. During COVID-19 pandemic, our Institute web server has been fiercely attacked (still going on sometime) and out Institute decided to close down some web pages and databases including the our bat virus database. I'v no idea when it will be open.
2. We have studied bat viruses for more than 15 years. All our work regarding the different type of bat coronavirus (partial sequences or full-length genome sequences) have been published and the sequence and sample information have been submitted to GenBank. You can find our publications and sequence information by your own and do your own analysis to satisfying your curiosity. But I would like to remind you to ask the help from a coronavirologist in avoiding of misunderstanding what we have done.
3. During 15 years, we only isolated 3 bat coronaviruses (virus can grow in cell culture in the lab) and all of them has been published in the international journals. The other bat coronaviruses are known from their genomic sequences. Again, I would like to remind you to ask a virologist to help you to understand the difference between a live virus and a genomic sequence.
4. I don't understand why there are some people in this world lost trust to sciences and scientists. The sciences need prove but the conspiracy don't because no one can prove a conspiracy.
5. I'll not answer any of your questions if your curiosity is based on the conspiracy of "man made or lab leak of SARS-CoV-2" or some non-sense questions based on your suspicion. No trust, no conversation.
Best regards,
Zhengli Shi
-----原始邮件-----
发件人:"Tommy Cleary" <tommy.cleary1@my.nd.edu.au>
发送时间:2021-01-26 01:44:31 (星期二)
收件人: "Jane Euler" <jeuler@cnri.reston.va.us>, "中文DOI运维" <doi_om@istic.ac.cn>
抄送: "Catherine Rey" <crey@cnri.reston.va.us>
主题: RE: Missing DOI “Wildlife-borne Viral Pathogen Database” Shi Zhengli of the Wuhan Institute of Virology
Jane Euler jeuler@cnri.reston.va.us
Dear Jane,
Thank you for your reply.
Can you confirm the article
“Wildlife-borne Viral Pathogen Database”
Is hosted by this DOI
by Shi Zhengli of the Wuhan Institute of Virology
Zheng-Li Shi zlshi@wh.iov.cn
Can you please confirm when
the DOI was registered and to whom
it was registered etc?
The WIV team published amazing papers such as
“Bat Severe Acute Respiratory Syndrome-Like Coronavirus WIV1 Encodes an Extra Accessory Protein, ORFX, Involved in Modulation of the Host Immune Response”
https://jvi.asm.org/content/90/14/6573/article-info
This type of paper shows this data base of SARS-like Coronavirus from bats holds information about the origins of the current COVID19 pandemic and the way features of the codes of these CoV viruses can help understand the type of medicine needed to help people survive when infected.
Any information that you can give, however mundane, can help save lives and reduce suffering of this current pandemic.
Even taking the time to explain the limits (legal or otherwise) of what you can provide about DOI numbers is helpful.
Thank you Jane. Have a great day.
Kind regards
Tommy Cleary