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Response to Phoenix61 (Reply #10)

Fri Apr 16, 2021, 03:39 PM

19. No, I am not certain of that at all

Last edited Fri Apr 16, 2021, 04:39 PM - Edit history (1)

In fact, I am fairly confident that the virus has a natural evolution and that transmission was zoonotic.

But what intrigues me is the cover-up. When someone goes to great lengths to obscure something, there's a reason.

When I received my scientific training, one of the most valuable tips I learned was to design experiments as though you were trying to *disprove* your favored hypothesis. To approach your studies as a contrarian--because your peer reviewers will most certainly be doing so. It's the best way to try to ensure a balanced perspective, to fight against our natural inclination towards confirmation bias.

So that partly explains my approach to this. The other part, as I described above, is my observation of odd behaviors on the part of the CCP regarding this question on origins. That set off major alarms for me.

In terms of the Nature citation issue: nobody will ever convince me that it was trivial. Even for a "rushed" paper. Especially because of the surrounding circumstances: it was Shi's own prior work that deserved the cite. One thing I can absolutely guarantee you: no scientist, especially when writing a paper for Nature, omits an opportunity to cite their own published work. Go ahead and ask any/every scientist you know if that is a fair statement. Not to mention that the piece of data in question (RaTG13 sequence) was the central, pivotal piece of data proving the paper's thesis: that the newly discovered infectious agent was a bat coronavirus. Why not mention that you know this because your lab collected that specimin back in 2013 inside of a mineshaft where, just months prior, six workers contracted a mysterious respiratory disease--that would kill three of them--and that you partially sequenced that specimin and published about it in 2016? I mean, that is the normal way for a scientist to report a finding.

Below is the Addendum, published a full nine months later. See for yourself. There's nothing relevent in there that wasn't known in Feb 2020, and the critical citation I'm so concerned with is right there, too--Ge et al (2016). Why the nine month delay? Aren't you even a little bit curious?

Published: 17 November 2020

Addendum: A pneumonia outbreak associated with a new coronavirus of probable bat origin

Peng Zhou, Xing-Lou Yang, […]Zheng-Li Shi
Nature volume 588, pageE6(2020)

Here we provide further information about the bat SARS-related coronavirus (SARSr-CoV) strain RaTG13 reported in our Article. Between 1 July and 1 October 2012, we received 13 serum samples collected from 4 patients (one of whom was deceased) who showed severe respiratory disease. These patients had visited a mine cave in Tongguan town, Mojiang County, Yunnan Province, China, to clean bat faeces in order to mine copper before being admitted to the First Affiliated Hospital of Kunming Medical University on 26–27 April 2012. The samples we received were collected by the hospital staff in June, July, August and September 2012. To investigate the cause of the respiratory disease, we tested the samples using PCR methods developed in our laboratory targeting the RNA-dependent RNA polymerases (RdRp) of Ebola virus, Nipah virus and bat SARSr-CoV Rp3, and all of the samples were negative for the presence of these viruses. We also tested the serum samples for the presence of antibodies against the nucleocapsid proteins of these three viruses, and none of the samples gave a positive result. Recently, we retested the samples with our validated enzyme-linked immunosorbent assay (ELISA) against the SARS coronavirus 2 (SARS-CoV-2) nucleocapsid protein—which has greater than 90% amino acid sequence identity with bat SARSr-CoV Rp3—and confirmed that these patients were not infected by SARS-CoV-2.

We suspected that the patients had been infected by an unknown virus. Therefore, we and other groups sampled animals including bats, rats and musk shrews in or around the cave, and found some alphacoronaviruses1 and paramyxoviruses2. Between 2012 and 2015, our group sampled bats once or twice a year in this cave and collected a total of 1,322 samples. From these samples, we detected 293 highly diverse coronaviruses, of which 284 were designated alphacoronaviruses and 9 were designated betacoronaviruses on the basis of partial RdRp sequences. All of the nine betacoronaviruses are SARSr-CoVs, one of which (sample ID4991; renamed RaTG13 in our Article to reflect the bat species, the location and the sampling year) was described in a 2016 publication1. The partial RdRp sequence (370 bp) of ID4991 was deposited in GenBank in 2016 under accession number KP876546. All of the identified bat SARSr-CoVs are distantly related to SARS-CoV based on partial RdRp sequences. 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.

Ge, X. Y. et al. Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft. Virol. Sin. 31, 31–40 (2016).

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