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Eric • 1 year ago

Based on the fact it was submitted on January 20, 2020 and subsequently published on February 3, 2020, I could not fathom how it had been peer-reviewed so quickly. Upon further examination, I discovered that it has not been peer-reviewed at all. Per the publisher's website: "All peer-reviewed content will carry an anonymous statement of peer reviewer acknowledgement, and for those reviewers who give their consent, we will publish their names alongside the published article." No such statement exists for this article. I find this to be very odd, considering that this research has more than 2,300 citations and helped lay the foundation for the entire world community to declare an emergency of such remarkably unprecedented proportions.

https://www.nature.com/natu...

https://www.nytimes.com/201...

By comparison, see the "Peer review information" of a random article I selected in the Nature scientific journal about HIV research: "Nature thanks Nicolas Chomont, Philippe Lemey and the other, anonymous, reviewer(s) for their contribution to the peer review of this work."

https://www.nature.com/arti...

Acron Naji • 2 years ago

According to Shi's response to Science magazine, and her TV interview before, she doesn't have the isolated RaTG13 virus and any samples at her lab in Wuhan. This means there is no way to requecence RaTG13 scientifically and verify it existed or not in nature. Since it's crucial for the seeking of origin of SARS-Cov-2, I personally call for her retracting of this article.
https://www.sciencemag.org/...

Alberto Maria Cattaneo • 2 years ago

I also realized some inconsistency about the information available for RaTG13, have a look at my preprint on Researchgate: https://doi.org/10.13140/RG....

Zhou et al. mention to have collected RaTG13 samples from bats of the Yunnan province on 2013, but checking on GISAID, and all the other databases, RaTG13 was deposited only on 2020, no evidences that it was really sampled 7 years ago are available, apart "saying so".
Plus, in my preprint, I sequence-aligned the S-proteins of Covid-19 and RaTG13 with other Sars-Covs´, including Pangolin´s (Zhang et al. 2020 https://doi.org/10.1016/j.c... and I did not validated the same identity of the binding motif of the RBD that Zhang describes, neither I found evidences of the existence of a putative furin recognition motif in the S-proteins of Pangolin´s viruses.

All together, this rise further doubts about the origins of RaTG13. Supplementary evidences about the Sars-CoV-2 origins from Zhou et al. would be really appreciated.

Monali C. Rahalkar • 2 years ago

We have published a critical view on this paper in our preprint: https://www.preprints.org/m...

Samuel Soroaster • 2 years ago

How could this ever get published in Nature? Did the reviewers not note that the most important reference namely the RATTG13 Sequence happend to be published by the same lab only a few days before publication? Why would they wait 7 years only until after the outbrake in Wuhan to publish the RATTG13 sequence? This needs to be followed up by the editor. https://www.ncbi.nlm.nih.go...

prajwol • 2 years ago

I could not find accession numbers of reference sequence data that were used in phylogenetic analysis. If I were to replicate this study, how am I supposed to do so without any metadata table of the GenBank accession numbers of those reference sequences? How can Nature journal ignore these important component?

Kenneth McDonald • 2 years ago

I just wrote this to Health Feedback.org
QUOTE: "Covid-19 death predictions were wildly exaggerated by Imperial College. This helped to unreasonably form the idea lockdowns should occur in the Third World that will cause tens of millions of innocent women, children and babies to starve to death, in vastly higher numbers than the elderly might be saved to live a bit longer.
I agree the article "Manufactured Pandemic" did not have enough supporting evidence in it to prove some of its claims. All that proves is the article was badly written, not that the PCR Test did not at first have inefficient primers, or other possible failures. Your "refutation article" is being used to block anyone wanting to prove that they CAN come up with evidence missing from the Manufactured Pandemic article, as if you disproved the test has flaws, when all you proved was the article never had proof links.
Similarly Flora Teoh made the accusation the writer of the article was attacking Kary Mullis brilliant PCR technology, when all he/she was attacking was its particular use in this test. You then went on to say the person was "therefore" denying PCR can ever show viral load in OTHER tests or when he/she never. The ISSUE was did that specific test show viral load? As f it never we all have perhaps 10 viruses in our bodies in low viral load that do us no harm, (as Dr Andrew Kaufman points out) thus without viral load indication IN THAT ACTUAL TEST the test proves next to NOTHING.
You then allow no comments.
Do you realise that if you are saying the first 1 - 3 million stats are accurate when they are not that those stats (I believe are bogus) are being used to starve to death TENS OF MILLIONS of children in the Third World? AND your work is being used to stifle freedom of speech as well? Then you allow no comments to refute you?
Please reply to this message."

Kenneth McDonald • 2 years ago

Why is it that only one scientist, Flora Teoh, steps forward and says the PCR Test used on the first 3 million SARS-CoV-2 infections and death rate statistics is accurate, and shows viral load? Why don't hundreds step forward and put their reputations on the line? If Flora Teoh has this wrong, then the stats used to propose lockdowns in the Third World are bogus and unreliable, yet those lockdowns are said to cause an extra 20 million deaths of innocent women and children from starvation, as well as ruining the world economy so much we can barely help the millions of others who would usually be in danger of starvation. Thus it is MEGA important these PCR Tests are accurate, but we get ONE scientist stepping forward to tell us they are. Why?

Flora Teoh..... do you realise what you have done if you have this wrong???? MILLIONS OF CHILDREN AND BABIES may unnecessarily die in agony!

In my opinion she uses a reprehensible and clearly false tactic. She accuses the writer of the "Manufactured Pandemic" article of attacking the brilliant science of Kary Mullis of PCR in general. That is nonsense. I do not believe that for one second. The person obviously just thinks the SARS-CoV-2 Test method of use is wrong, especially if Kaufman is right that they compare the RNA they extract to an equally corrupted SARS-CoV-1 RNA strand, and it's only 80% similar.

Kenneth McDonald • 2 years ago

If anyone tries to post the now famous article "Manufactured Pandemic" on Facebook, they are threatened by Facebook, and a link to Flora Teoh's article "PCR tests for COVID-19 are specific for the novel coronavirus SARS-CoV-2 and do not detect other coronaviruses, contrary to claims in viral article and video" is forced onto the post as a supposed refutation.
Central to her claim the quick fix PCR test is accurate is her claim quote "Thanks to the efforts of scientists, we now know the full genome of SARS-CoV-2 [1]" and the link to "prove" this goes here. Can anyone here drag and drop a reply to me to show the "proof" of that from this article with a quote from it please?
If they span out in a centrifuge the SARS-CoV-2 virus, and mapped its RNA. it helps prove the credibility of the PCR Tests for SARS-CoV-2 detection, but not viral load. But if they really did isolate the virus that way, why not then put it in a healthy person and cause the disease and fulfill either the Koch's or the River's postulates? That Dr Andrew Kaufman says have not been fulfilled, so therefore calling SARS-CoV-2 an infectious disease is outside of accepted science. So when did you fulfil the River's or Koch's postulates? (several questions there).

Rossana • 2 years ago

The RdRp of RaTG13 has 100 % identity with the sequence BtCoV/4991
(KP876546) identified by Ge and colleagues in a Rhinolophus affinis bat in the
Yunnan province in 2013 as RaTG13. https://doi.org/10.1007/s12...
BtCoV/4991 is a novel beta-CoV, clearly separated from all known alpha- and beta-CoVs at that time. BtCoV/4991 differentiates from other bat CoVs also in the phylogenetic analysis carried out by Wang and colleagues https://doi.org/10.3390/v11...
Chen and colleagues identified BtCoV/4991 as the closest sequence to SARS-CoV-2 because RaTG13 had not yet been published at that time doi:
10.1080/22221751.2020.1725399.

How do BtCoV/4991 and RaTG13 relate to each other?

BatCoV • 2 years ago
Jodie • 2 years ago

Can we pm re these?

Sung-Joon Park • 2 years ago

We performed a metagenomic approach with WHU RNA-seq data;
https://www.nature.com/arti...,
(https://openlooper.hgc.jp/s...).

Of note, WHU01 (SRR10903402) RNA-seq reads included statistically significant "Mycoplasma"-related reads, and the most probable species was "Mycoplasma hominis", while "Streptococcus"-related reads are probably not the human pathogen (contamination?) (https://openlooper.hgc.jp/f....

Although this paper has used virus genomes, we have prepared the subsets of the RNA-seq reads that could not be mapped to the human genome and over 325,000 RefSeq microbial genomes (inc. SARS).

Over 80% of the subset reads (R1 only) could be mapped to the nCoV genome (NC_045512), which may be greatly useful to characterize nCoV specific genome.

madmaxNY • 2 years ago

Wow, unbelievable that this passed editorial and peer review at Nature! Something very strange that they would rush a paper out that is even not seriously edited, with tons of grammatical errors, so how many scientific errors either intentional or otherwise? Reviewers, please identify yourselves and release your reviews, the extent to which you went to validate the results, whether you had access to the raw sequence data, etc. And as cases continue to be made that the senior author on this paper, Zheng-Li Shi, has spent her career engineering this type of virus, publishing papers on the ability to do this and so on:

https://www.zerohedge.com/g...

I guess the editors at Nature did not feel it necessary to question the integrity of these results and force a more in depth review and replication from others.

bioconductor Sun • 2 years ago

Where can the scientist world-wide get the raw NGS reads to review and re-analyze the squencing data?

Duhnkuhn Hussein • 2 years ago

Zheng-Li Shi will end up killing more people that Mao Zedong. That is impressive.

ben • 2 years ago

How so?

Jason • 2 years ago

some key data and logical connection is missing in order for the author to claim "We then found a short RdRp region from a bat coronavirus termed BatCoV RaTG13 which we previously detected in Rhinolophus affinis from Yunnan Province showed high sequence identity to nCoV-2019."

BiologyGeek • 2 years ago

Tens of thousands of people are infected and hundreds died. We need to better understand how the bat coronavirus got transmitted to human patients in this 2020 outbreak. Many blame a wildlife market in Wuhan - but there are 661 cities in China and many of them, especially 41 in Guangdong where residents are known to like bushmeat, have such markets. Why didn't the outbreak start from any of the other 660 cities, especially the 41 in Guangdong - but why Wuhan? For example, the 2002-2003 SARS outbreak started from Fushan, Guangdong, but not Wuhan.

Moreover, according to Figure 1 of China CDC's recent report: https://www.nejm.org/doi/fu..., the first two patients had no link to the Wuhan wildlife market at all.

Now, if you look at this: there are 661 cities in China, but there is only one city, Wuhan, hosting a biosafety level 4 (BSL-4, or P4) lab. It's the only lab in China that captures bats and is authorized to study the bat coronavirus. The authors, as part of this BSL-4 lab, started to do so since 2015. Statistically, the bat coronavirus of the Wuhan outbreak is more likely to be from the only Wuhan BSL-4 lab that studies bat coronavirus in China, as opposed to be from the wildlife markets - Wuhan's wildlife market is among hundreds of wildlife markets existing in hundreds of cities in China. Is there any possibility that the bat coronavirus got leaked from this BSL-4 lab unintentionally through improper handling of samples and lab animals? This needs to be investigated.

BiologyGeek • 2 years ago

An update on the questions on the origin of the coronavirus:

A recent news reported that China has denied the lab link to coronavirus. https://www.washingtontimes... "However, a Chinese government-funded study published Jan. 24 in the medical journal The Lancet by 29 Chinese scientists found that 13 of 41 victims surveyed had no connection to the wild animal market. Significantly, the first patient identified with the coronavirus was a man who reported pneumonia-like symptoms on Dec. 1 but had no connection to the market."

The mentioned Lancet paper is here: https://www.thelancet.com/j...

Who is the first patient? What happened to him? How come he had no link to the market? Why the coronavirus he contracted with "showed high sequence identity" to the "BatCoV RaTG13" stored in the lab of the authors?

BiologyGeek • 2 years ago

Also, we need to note that, as recently publicly pointed out by Dr. Yi Rao, President of Capital University of Medical University in China, Mrs. Yan-yi Wang - the Lab Director of the Wuhan BSL-4 lab as well as the supervisor of Dr. Zheng-li Shi - is professionally not qualified. News is here: https://www.backchina.com/n....

Moreover, the concern about the safety issue of the Wuhan BSL-4 lab was discussed as early as in 2017: https://www.nature.com/news...

The authors of this article are from the questioned Wuhan BSL-4 lab. The safety concern is serious. The possibility of an unintentional bat coronavirus leak causing this 2020 coronavirus outbreak should be at least discussed and investigated.

Michael Siedel • 2 years ago

just a few questions? 22 pages seven test persons only one had the virus detectable! all slight fever! 96 percent match! the rest of the other ingredients thrown together wildly? who cross-checks which laboratory level 4? why 9 days until approval by Nature, since submission when it is urgent? and then another 4 to upload 22 pages? Thank you very much! yes always the bats and always the markets and always test environment Wuhan! Dankeschön ihr Hausmeister Krause/ #fafnör
Michael Siedel member MinD Germany number 21165

lindsey rim • 2 years ago

i dont know what your talking about, but read this article plz if you know nothing about the coronacirus https://www.ladieshabits.co...

Parvaiz • 2 years ago

Nitazoxanide as a possible agent for the 2019-Novel Corona Virus infection
Isolation of the virus and testing of antiviral drugs is critical to the management of the cases at present as this outbreak seems to have shaped clearly worse than the SARS and the MERS-coV outbreaks reported in the earlier parts of this century. This would allow studying the antiviral efficacy of various antiviral agents against the virus. Pertinently combinations of antiviral agents can be tried. Additionally the antiparasitic agent nitazoxanide might be useful and may be worthwhile testing in patients who are sick based on the premise that the combination of nitazoxanide and oseltamivir was found to be superior to oseltamivir alone in influenza patients in a previous study. Nitazoxanide is a safe antiparasitic agent, widely prescribed and has been demonstrated to have antiviral properties which could be exploited in the current settings to treat severe cases in combination with investigational antiviral agents as also test its efficacy in the laboratory against cultured virus isolates.