CROWDSOURCING: Why is a sequence in the Fan Wu paper continually cited as being "the" reference sequence -- and why is it assumed a single reference informed anything?
Over the past couple of months I’ve spent time reviewing early published papers from Chinese scientists on 2019-nCoV-2019/SARS-CoV-2 and making changes to a timeline I published last summer.
Although some of the methods in the papers are “above my pay grade” — i.e., beyond my current level of speciality/expertise — I am left with some things I still don’t understand but want to understand.
A recent article on
— SARS-CoV-2 Fragments of Fiction: How Mathematical Fraud and Genetic Sequencing Manufactured a Global Crisis by Michael Wallach — brings one of these things to mind.He writes:
When we remember that this Fan Wu paper formed, in essence, the bedrock of the “scientific” foundation of the claimed pandemic, it’s hard to say whether one should laugh or cry. It was upon the conclusion of this paper that the PCR testing was designed, and the world was tested for this “novel virus.” It was upon this paper that synthetic “virus” sequences were built by laboratories to test the “virus” for its qualities and to study its “nature.”
I would love to hear from readers who have a) read the study and b) considered events in this and/or other relevant timelines and can explain why it is often said a sequence from the above study was the single reference for anything.
Comments are open; anyone with an informed, relevant response can reply.
Irrelevant comments will be removed at my discretion. This is a genuine crowdsourcing effort aimed at gathering insights from those who’ve “done the homework” and can help me answer a question — one that may have an obvious answer I’ve simply overlooked.
Suggestions for revisions/additions to timeline below also welcome.
I am noticing that the pre-print and published versions of the paper that classified and (re)named 2019-nCoV as SARS-CoV-2 include the following acknowledgement:
(Pre-Print https://www.biorxiv.org/content/10.1101/2020.02.07.937862v1.full) "The authors gratefully acknowledge the work of all researchers who released SARS-CoV-2 genome sequences through the GISAID initiative and particularly the authors of the MN908947 genome sequence."
(Published version https://www.nature.com/articles/s41564-020-0695-z ) "We thank all researchers who released SARS-CoV-2 genome sequences through the GISAID initiative and particularly the authors of the GenBank MN908947 genome sequence: F. Wu, S. Zhao, B. Yu, Y. M. Chen, W. Wang, Z. G. Song, Y. Hu, Z. W. Tao, J. H. Tian, Y. Y. Pei, M. L. Yuan, Y. L. Zhang, F. H. Dai, Y. Liu, Q. M. Wang, J. J. Zheng, L. Xu, E. C. Holmes and Y. Z. Zhang.
Why was "that" sequence the one that received the ICTV-CSG's attention (although more than one sequence was obviously being looked at)?
I may need to re-read those papers -- and the emails in my own article. https://www.woodhouse76.com/p/the-sars-cov-2-name-game-long-read
"Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China."
Since the first SARS outbreak hoax in 2002, they always fishing for such 'virus' sequences and they decided this time it was a bingo.