TruthArchive.ai - Tweets Saved By @stevenemassey

@stevenemassey - Steve Massey

Zhengli Shi of the WIV constructed a dangerous Gain of Function MERS chimera that contaminated pre-pandemic rice sequence datasets from Wuhan Potential violation of the Biological Weapons Convention NIAID + USAID provided funding Parallels with SARS2 🧵 #DRASTIC https://t.co/mrFgW2eSR3

@stevenemassey - Steve Massey

The Zhang group of Fudan University have identified and validated two A-B intermediate SARS2 genomes from the early pandemic This provides a key to understanding the origin of COVID19 🧵

@stevenemassey - Steve Massey

2/ In their new paper, the Zhang group sequence 343 new SARS2 genomes from the early pandemic (sampled up to Oct 2020). The genomes were obtained from COVID19 patients in the Shanghai Public Health Center https://academic.oup.com/ve/advance-article/doi/10.1093/ve/veae020/7619252?login=false

@stevenemassey - Steve Massey

3/ Importantly, they identify two SARS2 genomes intermediate between lineage A and lineage B These were validated using two methods, RT-PCR (Sanger sequencing), and Next Generation Sequencing (NGS). @jbloom_lab verified the sequencing depth on one (high)

@jbloom_lab - Bloom Lab

Zhang uses term “B0” to designate T8782 / T28144 sequences intermediate between clades A and B, and provides deep sequencing data to support their existence. (I re-analyzed SRR25229357 & found T supported by 5776/5807 high-quality base calls at 8782, and 62,353/62,608 at 28144)

@stevenemassey - Steve Massey

3/ What is an A-B intermediate genome and why is it important ? Lineages A and B were the first major lineages to emerge during the early pandemic. They are only separated by two mutations, at positions 8782 and 28144

@stevenemassey - Steve Massey

4/ Lineage A is T8782 /C28144 (T/C) while lineage B is C8782/T28144 (C/T) The closest related bat CoVs are T/C implying A is ancestral A and B interconverted via a single mutation, either via C8782 / C28144 (C/C) or T8782/T28144 (T/T)

@stevenemassey - Steve Massey

5/ The existence of either a T/T or C/C intermediate in the human population would indicate that this interconversion occurred after SARS2 entered the human population, supporting a single introduction This is why intermediates are key to understanding the origin of the pandemic

@stevenemassey - Steve Massey

6/ The two T/T intermediate genomes sequenced by the Zhang group from patients infected in Henan and Shanghai and hospitalized on Feb 4th and Feb 8th 2020 respectively

@stevenemassey - Steve Massey

7/ These are related to 7 T/T genomes in the db: 2 from Wuhan, 4 from Singapore and 1 from the UAE Notably, 3 of these are identical to the two new T/T intermediates sequenced by the Zhang group, and 3 more only differed by a single SNV

@stevenemassey - Steve Massey

8/ The widely cited Pekar et al (2022) posited that there were two separate introductions of lineage A and B, in the Huanan Seafood Market (HSM) A major plank of their thesis was the claimed absence of true intermediate sequences https://www.science.org/doi/10.1126/science.abp8337

@stevenemassey - Steve Massey

9/ However, @humblesci @Daoyu15 @ydeigin @quay_dr and myself previously showed that their exclusion criteria were flawed, and that several potential intermediates were improperly excluded by Pekar et al https://www.mdpi.com/2036-7481/14/1/33

Unwarranted Exclusion of Intermediate Lineage A-B SARS-CoV-2 Genomes Is Inconsistent with the Two-Spillover Hypothesis of the Origin of COVID-19 Pekar et al. (2022) propose that SARS-CoV-2 was a zoonotic spillover that first infected humans in the Huanan Seafood Market in Wuhan, China. They propose that there were two separate spillovers of the closely related lineages A and lineage B in a short period of time. The two lineages are differentiated by two SNVs; hence, a single-SNV A-B intermediate must have occurred in an unsampled animal host if the two-spillover hypothesis is correct. Consequently, confirmation of the existence of an intermediate A-B genome from humans would falsify their hypothesis of two spillovers. Pekar et al. identified and excluded 20 A-B intermediate genomes from their analysis. A variety of exclusion criteria were applied, including low read depth and the assertion of repeated erroneous base calls at lineage-defining positions 8782 and 28144. However, data from GISAID show that most of the genomes were sequenced to high average sequencing depth, appearing inconsistent with these criteria. The decision to exclude the majority of genomes was based on personal communications, with raw data unavailable for inspection. Multiple errors, biases, and inconsistencies were observed in the exclusion process. For example, 12 intermediate genomes from one study were excluded; however, 54 other genomes from the same study were included, indicating selection bias. Puzzlingly, two intermediate genomes from Beijing were discarded despite an average sequencing depth of 2175X; however, four genomes from the same sequencing study were included in the analysis. Lastly, we discuss 14 additional possible intermediate genomes not discussed by Pekar et al. and note that genome sequence filtration is inappropriate when considering the presence or absence of a specific SNV pair in an outbreak. Consequently, we find that the exclusion of many of the intermediate genomes is unfounded, leaving the conclusion of two natural zoonoses unsupported. mdpi.com

@stevenemassey - Steve Massey

10/ This included 4 potential T/T intermediates, 3 of which were noted by the Zhang group (EPI_ISL_462306, EPI_ISL_493180 and EPI_ISL_493182) In our paper we argue all four were improperly excluded, on the basis of personal communications, and abitrary use of depth cutoffs

@stevenemassey - Steve Massey

11/ The fourth, EPI_ISL_493179, was not mentioned by the Zhang group, but was from Wuhan and part of the same study that generated EPI_ISL_493180 and EPI_ISL_493182) It differs from Hu-1 at C8782T, T13402G

@stevenemassey - Steve Massey

12/ In addition, with @WashburneAlex we identified an additional T/T intermediate was not considered at all by Pekar et al (or the Zhang group) This was OM065349 (Genbank Accession), sampled in Lu'an, Anhui on 30 Jan 2020 from a 53 yr old female https://www.biorxiv.org/content/10.1101/2022.10.10.511625v1

Statistical challenges for inferring multiple SARS-CoV-2 spillovers with early outbreak phylodynamics bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution biorxiv.org

@stevenemassey - Steve Massey

13/ This genome is identical to the 2 new T/T intermediates from the Zhang group In total, there are 4 intermediates in the db that differ from Hu-1 only at C8782T (that gives the T/T genotype) and are identical to the 2 new T/T intermediates from Zhang et al

@stevenemassey - Steve Massey

14/ So, there are 6 identical T/T intermediates, sampled from a variety of locations in and outside China, early in pandemic

@stevenemassey - Steve Massey

15/ Why is this important ? The existence of T/T intermediates in the human population indicates a single introduction of SARS2 1) This confirms that lineage A is ancestral This is because A is T/C, the same as the closest related bat CoVs

@stevenemassey - Steve Massey

16/ 2) This excludes the HSM as source of the spillover This is because the genomes sequenced from the HSM were almost all B, which is derived, as opposed to A, which is ancestral

@stevenemassey - Steve Massey

17/ 3) This indicates a date of emergence of no later than ~ Oct 2019, as per Kumar et al This is based on the number of mutations needed (3) to get to proCoV2 from the lineage B reference sequence (Hu-1) https://academic.oup.com/mbe/article/38/8/3046/6257226

@stevenemassey - Steve Massey

18/ Finally, a further potential clue to the origin of the pandemic is presented by our preprint by @humblesci @Daoyu15 @BiophysicsFL @ydeigin @quay_dr and myself characterizing a MERS-related infectious clone from Wuhan 2019 that has undergone apparent GOF experimentation

@stevenemassey - Steve Massey

19/ It was recently turned down from a journal for non-scientific reasons, in an apparent failure of nerve on the part of reviewers and editor https://www.biorxiv.org/content/10.1101/2023.02.12.528210v2

Discovery of a novel merbecovirus DNA clone contaminating agricultural rice sequencing datasets from Wuhan, China bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution biorxiv.org

@stevenemassey - Steve Massey

20/ Are there any journal editors out there brave enough to give our manuscript a fair hearing ? https://t.co/AS9YRH7hRb

@stevenemassey - Steve Massey

21/ @threadreaderapp unroll