"currently available data" is highly biased (at best). If you conclude something from biased data, your conclusions will be biased.
A good scientist assesses quality and biases of data first. That is how Science work
If you do not study something enough, you do not make an absolute judgment, much less give extreme probabilities. There you exceeded your mandate and did something unprofessional.
[Thread] New unforced error. GIABR, the lab of the pangolins, has just uploaded sequences (MW600658:MW600715) that shows a trip to the Mojiang mineshaft or nearby on 22-Aug-2017, well after the last known trip of WIV in 2015.
Libiao Zhang explicitly credited as collector.
Some context: Very few CoVs published with collection date after 2016 by Chinese institutions
[Thread] Who is the first known patient?
There is a lot of confusion, so let's review all possible patients according published onset dates [of symptoms] up to 15-Dec-19.
Patients are anonymized, so they are identified as <AgeSex> (e.g. 49F is a 49-year-old female). In case there are many patients with same age & sex, suffixes are used (e.g. 65M1, 65M2, ...).
U = Unknown.
Problem: people can have birthday during illness
XX Su (61F), XX Wang (62M) & XX X (UU) onset 14, 21 & c. 30-Nov-19.
Info unnoticingly leaked in Health Times and uncovered by DRASTIC and @ianbirrell
[Thread] Necessary corrections to the China-WHO report.
What they will probably fix and what they will not.
TLDR: circular swap of 3 IPCAMS genomes + tampered onset of Wuchang accountant; First patients and first cluster; Some falsehoods in articles washingtonpost.com/world/asia_pac…
As we said, the problems were with S01, S05 & S11. Absolutely chaotic, but with a little table it is all more clear. Part of the problem is inherited from Ren et al. (2020) who followed different orders in the text and in the genomes for the patients.
Jan 7, 2021, AVC Panel Discussion Origins of SARS-CoV-2 (from @KatherineEban's article)
“the incredible difficulty of isolating live virus from bat samples, which are usually fecal samples, and that this is extremely unreliable and usually not successful” downloads.vanityfair.com/lab-leak-theor…
"The mounting evidence that the COVID-19 coronavirus escaped from the WIV, rather than spontaneously emerging from nature, had become the hottest topic in journalism and potentially the most consequential science story in a generation" commentarymagazine.com/articles/james…
"The COVID-19 pandemic revealed a profound corruption at the heart of our expert class. The impact of that revelation will reverberate for years to come"
"“The DRASTIC people are doing better research than the U.S. government,” a State Department investigator told Vanity Fair"
The previous mainstream narrative of "anything outside of a zoonosis is a conspiracy theory" was built upon two letters (not articles), among most cited papers of the year. Even Dr. Shi used them. They are both sinking now.
1/ The proximal origin of SARS-CoV-2
The corresponding author is self-debunking, and a co-author was de-facto retracting
2/ Lancet's letter (or Daszak's letter)
It did not fare any better. It was proved orchestrated by @PeterDaszak and, AFAIK, at least three co-authors de-facto retracted publicly declaring that the question of the origin was open
They finally concede after more than a year: "Here, we report the identification of a novel lineage of SARSr-CoVs, including RaTG15 and seven other viruses, from bats at the same location where we found RaTG13 in 2015"
No mention to the miners or the mine. Just this: "in Tongguan town, Mojiang county, Yunnan province in China in 2015, the same location where we found bat
RaTG13 in 2013"
1/ MSc thesis of Wang, 2nd co-author of the article of the first 4 trips to the mine (Ge et al., 2016), and dated 2 years before this article and can be considered as some of the first steps of this research
She states that "fever patient sera were obtained from a hospital in Yunnan Province". Very vague description! But later, in the Fig 2.6 there is an important clue: samples are named as "MJ123", using one of WIV standard naming formats...
[Thread] In-silico molecular overclocking of RaTG13.
TLDR: 191-nt RdRp segments of SARS-CoV-2, RaTG13 and Ra7896 show an unexpected molecular clock behavior. In-silico synonym mutations is one probable explanation.
Assuming SARS-CoV-2 is an ancestor of Ra7896 (used in RaTG13) does not fully explain it. Implied evolutionary rate would be in the order of 10^-2 substitutions/site/year in a well-conserved part of the genome, far from a normal ~10^-3 for a complete genome
So, it is not only SARS-CoV-2 having its molecular clock frozen, but also RaTG13 molecular clock running more than expected. @nerdhaspower and @quay_dr have already noted strange patterns of synonym mutations along the genome of RaTG13
[Thread] Pangolin CoV... or Bat CoV in pangolins samples?
TLDR: A researcher of the team that sequenced the pangolins samples had taken samples in the mine of RaTG13 and in the place where RmYN02 was collected, also catched bats in Yunnan. Probably contaminated pangolin samples
@Daoyu15 was the first to note that the raw sequence reads of the pangolins “contained unexpected reads and was in serious risk of contamination” in early June 2020. But now we can explain how it was possible to happen this in Guangdong zenodo.org/record/4450267…
Jin-Ping Chen, the corresponding author of the first paper of the pangolins, and LiBiao Zhang, who has been sampling the mine of RaTG13 and the place in Mengla where RmYN02 was collected, are close colleagues in GIABR & GIZ ncbi.nlm.nih.gov/pmc/articles/P… giz.gd.cn/yjdw_/yjy/
@nature cc reviewer @c_drosten, this article must be corrected to acknowledge that SADSr-CoV 3755 was from the same mine of Mojiang (Yunnan) as RaTG13. Any reader of the paper thinks it came from Guangdong, and that is not true nature.com/articles/s4158…
As you see, its ID is in the middle of the IDs of the 1st trip of WIV to the mine (Ge et al, 2016).
Obviously, disclosing its full sequence is also a must, not only the N.
Wang et al. (2019) stated it was from Yunnan in their Fig 1.
Ra7347 most probably from the mine too. And 140351 too (they messed samples of May-14)
With so many errors, lack of info, cheatings and covers, the phylogenetic trees are totally useless! Shame ncbi.nlm.nih.gov/pmc/articles/P…