Flavinkins (@Flavinkins)

Additional sample formats, such as “bat coronavirus isolate NNNNNN” are found in 2015 samples, whereas the 2016 sequences (the last sequences to be deposited into GenBank from known bat coronavirus searching papers in China/CAS) contained within their authors “Edward C Holmes”. This may hint on the role of E.Holmes on the handling of bat Coronavirus sample sequencing for samples collected “between 2015-2019”. Sequences MH315932-MH315944 have formats “XxNNNNNN”, however these contained samples from as early as 2013, making it difficult to ascertain as where these samples came from. However, these numbers (and the “Spread and Geographic Structure of SARS-related Coronaviruses in Bats and the Origin of Human SARS Coronavirus” paper, with E.Holmes in the GenBank records) contained the only deposited CAS samples known to be collected in 2016, which could be taken as evidence of E.Holmes and WIV collaboration for sampling efforts and sequence/sample sharing, in the 2015-2019 period. A collaboration (sample/sequence sharing) between Guangdong and Wuhan institutions through E.Holmes https://zenodo.org/record/6849652#.Y38toiW8klT , can not be ruled out. The original GenBank deposition date of 2018 seems to coincide with the supposed sampling date of “BtSY2”. We now know that some of the samples taken in 2018 under E.Holmes contained RBD sequences related to the Omicron strain of SARS-CoV-2. The question becomes: Why you are taking samples from bats (dissected rectum), without performing some kind of tests immediately after sampling, as early as in 2015-2018, given that an ethics approval for the destructive sampling of wild animals in China required some kind of academic program to be first sent for approval, which have to include the detail of the exact experiments that requires the dissection of the bats and collection of the rectum samples. If any kind of testing/screening/experimentation were done initially on the samples (immediate experimental plan would have to be provided for the sampling proposal to be justified and approved—and “for storage, until some technology that doesn’t yet exist until late 2021” isn’t one of them), what were the results? Why, despite sampling of bats by EHA/CAS and expeditions into Yunnan/Mojiang mine continued all the way until 2019, the last such sequences deposited from China was sampled in 2016? If “This research, including the procedures and protocols of specimen collection and processing, 262 was reviewed and approved by the Medical Ethics Committee of the Yunnan Institute of 263 Endemic Diseases Control and Prevention. (No. 20160002).”, why weren’t the results immediately made available to the public as the samples were collected and processed over the course of 4 years? RNA samples are after all, very fragile and does not tolerate long-term storage very well. When were these actually sequenced? (I see 15 different sequencing machines in the FCIDs, with FCIDs ranging from H2 to H7, HG to HY, and sequencing on the same machines hundreds of runs apart. This could indicate sequencing done immediately after sampling) And if these were sequenced before the pandemic, who had access to the sequences? Were these really “newly discovered” viruses, or just sequences that were put into embargo in the “great silence” of CAS accession numbers between 2016-2019, only recently released? (Should these samples be sequenced pre-pandemic, near their collection date in 2018, this could be corresponding to phase 1(QS0) of DEFUSE. After sequences generated as early as in mid-2018, there would be more than 1 year to work with the cloning and culture experiments.) The machines found in https://github.com/Augustpan/Individual-Bat-Virome/blob/main/raw_data/lane_id_table.csv Are: A01426 A00821 A00920 A00270 A00877 A00289 A00881 A00783 A00253 A00917 A01045 A00808 A00459 A01415 A01050 The samples with BtSY2 are: S18CXBatR24 @A00917:648:H3Y25DSX2:4 S18CXBatR29 @A00783:739:H3V32DSX2:3 Both appeared to be on the earliest run on that particular machine, where the run contained no sample from 2019, and where the flow cell ID were from an early era (H3). Archive for read mappings: https://archive.ph/CuzzR Archive for lane IDs: https://archive.ph/IKxD1