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Steve Massey Profile picture
Steve Massey
@stevenemassey
Computational biologist and epistemic trespasser. I'm in it for the decentralization! #DeSci Currently studying the origin of COVID-19
Medical Science and Technology #earlytreatments Profile picture Steve Simpson Profile picture Misha🍉 who's the 6th all-seeing 👁 Profile picture justcheckinout Profile picture Loofymectin aka Jan Masleid Profile picture 9 subscribed
Apr 18 • 26 tweets • 7 min read
Differential gene expression analysis of the controversial RaTG13 dataset reveals strong similarity to the RaTG15 dataset, also described as generated from a Rhinolophus affinis 'rectal swab' from the Mojiang Mine

This indicates they have a common, undefined source 🧵 Image 2/ The source of the RaTG13 dataset has been a key puzzle of the C19 Origin debate

RaTG13 was sequenced by the Wuhan Institute of Virology prepandemic in 2017/2018 and remains the closest related CoV backbone to SARS2
Mar 8 • 22 tweets • 6 min read
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 🧵 Image 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
academic.oup.com/ve/advance-art…
Feb 13 • 10 tweets • 4 min read
Was Baric aware of the work on the human α-ENaC furin cleavage site (FCS) at the University of North Carolina (UNC) ? 🧵

In a striking coincidence, the human α-ENaC FCS is exactly the same as that of SARS2, as first noted by Anand et al in 2020
elifesciences.org/articles/58603 2/ Furin cleavage of human α-ENaC has been studied by M.Jackson Stutts, who is based at the UNC School of Medicine

Ralph Baric is also based at UNC School of Medicine, and also has an interest in lung disease. Was he aware of this work ?

rupress.org/jgp/article/15…
Jan 25 • 23 tweets • 7 min read
What was the restriction enzyme BsmBI, itemized in the DEFUSE budget, to be used for? 🧵

3 possibilities:

i) To make an spike ectodomain expression vector
ii) To insert recombinant S genes into VRP vectors
iii) To make infectious clones (ICs) Image 2/ I will consider each of these possibilities as follows
Jan 20 • 10 tweets • 4 min read
A potential explanation for the alanine (A684) in the SARS2 FCS ?

Alanine mutational scanning is used to systematically mutate residues in functional sites, to determine if they ablate function, so indicating their importance 🧵

en.wikipedia.org/wiki/Alanine_s… 2/ In the recent FOIA-ed DEFUSE documents released by @emilyakopp and @USRightToKnow there is a section that proposes to 'ablate' 'human-specific cleavage sites' introduced into SARSr-CoV spike proteins Image
Dec 18, 2023 • 4 tweets • 1 min read
Bombshell !

From an early draft of DEFUSE:

"The BSL-2 nature of work on SARSr-CoVs makes our system highly cost-effective relative to other bat-virus systems" Baric was aware of the lax safety standards at the WIV, in the following draft note:

" In china, might be growin these virus under bsl2. US reseachers will likely freak out"

But put his name to the proposal anyway
Dec 3, 2023 • 7 tweets • 2 min read
This statement about DEFUSE by Eddie Holmes is misleading. DEFUSE describes the identification of potential FCSs in the spike gene of SARSr-CoVs. FCSs are typically found at the S1/S2 boundary...... 🧵 Image 2/ To quote DEFUSE: 'We will analyze all SARSr-CoVs for appropriately conserved proteolytic cleavage sites in S2 AND (my capitals) for the presence of potential furin cleavage sites'
Aug 2, 2023 • 34 tweets • 9 min read
When were the only two known pre-pandemic SARS2-related live isolates (attributed to pangolins) isolated ? And when were they sequenced ?

And why does one of them have SARS2 reads in its sequence file ? 🧵 Image 2/ There has been a lot of interest in the provenance of the RaTG13 sequence, as it is still the closest related backbone to SARS2

ZC45 and ZXC21 were the only other known SARS2-related genome sequences generated in China pre-pandemic

Or were they .......?
Jul 18, 2023 • 22 tweets • 6 min read
A couple of snippets from the surprisingly sparse recent ODNI report on the origin of C19 consisted of the claim that the WIV worked on pangolin samples in 2019, and that there was PLA involvement in coronavirus research there 🧵
Image
Image 2/ Do they have some forensic genomic data or inside sources ?

Unfortunately maybe not - it seems that the pangolin claim may have derived from the recent 2023 paper by ZLS and Yigang Tong on infectivity characteristics of live pangolin isolate MpCoV-GX

journals.asm.org/doi/full/10.11…
May 10, 2023 • 24 tweets • 7 min read
A new animal coronavirus, possibly from bamboo rat, is present in abundance in sample Q61 from the Huanan Seafood Market

This find, however, stands in stark contrast to the single SARS2 read present in the same sample, which has a high proportion of raccoon dog sequences 🧵 Image 2/ Sample Q61 was generated by Liu et al in their survey of the Huanan Seafood Market

It has generated discussion for having a high level of raccoon dog reads, which has been postulated by some workers as an intermediate host for SARS2
nature.com/articles/s4158…
Apr 22, 2023 • 18 tweets • 5 min read
New coronaviruses in raccoon dog sample Q61 !!

On Blast searching individual reads from Q61 that matched the human OC43 and HKU1 genomes, the closest matches are to bamboo rat and rodent CoV sequences 🧵

h/t @babarlelephant @humblesci Image 2/ Previously I had found reads that mapped to human OC43/HKU1 coronaviruses, interpreting this to mean that human coronaviruses were present in the raccoon dog sample Q61
Apr 15, 2023 • 19 tweets • 8 min read
What is the true trace level of SARS2 in the raccoon dog sample Q61 from the Huanan Seafood Market ?

Here, in a refined analysis, I show that human common cold coronaviruses are present in quantities greater than SARS2 in Q61 🧵 Image 2/ Q61 is a key sample described by Liu et al in their survey of the Huanan Seafood Market, as it contained large quantities of raccoon dog sequences, leading some to claim that it was evidence that raccoon dogs were the source of the SARS2 pandemic
nature.com/articles/s4158…
Apr 6, 2023 • 20 tweets • 5 min read
In their survey of the Huanan Seafood Market, Liu et al conclude that there is no evidence for a zoonotic transmission of SARS2 at the market

Out of curiosity, I did a deep dive into sample Q61 (Env_0576), which they report as having a high proportion of raccoon dog reads 🧵 Image 2/ I ran a mitoscan analysis, a procedure developed with @humblesci , that was first described by Csabai and Solymosi in their Antarctic soil preprint that identified early SARS2 sequences associated with a variety of potential mammalian cell lines 👇
researchsquare.com/article/rs-133…
Mar 23, 2023 • 20 tweets • 8 min read
Our new paper on intermediate lineage A-B SARS2 genomes is out !

Within, we criticize the exclusion of 20 potential A-B intermediate genomes from Pekar et al (2022), finding that the majority were improperly excluded 🧵
mdpi.com/2036-7481/14/1… 2/ Lin(eage) A and lin B are two earliest established lineages from Wuhan. A likely arose first, with B arising from A via two SNVs at positions lineage defining positions 8782 and 28144 Image
Mar 21, 2023 • 4 tweets • 2 min read
9/ This saga is a case study in the perils of making grandiose claims without having completed the analysis, and of the hubris to embark into a new subject area without specialists (metagenomic) to scrutinize and suggest robust analyses 10/ The report can be found here:
zenodo.org/record/7754299…
Mar 21, 2023 • 12 tweets • 4 min read
So, Flo Debarre et al’s raccoon dog analysis that has caused such a media frenzy has been released and what does it show ?

Not much 🧵 2/ Essentially, it confirms Gao et al’s preprint analysis that there was nuc acid from animals in addition to humans in the samples 👇 (no surprise there)

It adds some species specific info
Feb 22, 2023 • 6 tweets • 2 min read
Here is a short summary of our recent discovery of a novel MERS-related coronavirus clone from Wuhan We identified an infectious clone of a novel MERS (Middle Eastern Respiratory Syndrome) related coronavirus (MERSr-CoV) in sequence datasets from Wuhan, China. @WashburneAlex provides his perspective here: alexwasburne.substack.com/p/an-unreporte…
Feb 21, 2023 • 15 tweets • 8 min read
We have uncovered evidence of undocumented GOF work in Wuhan 🧵

We have identified an infectious clone (IC) of a novel MERS-related coronavirus in rice sequencing datasets from Huazhong Agricultural University (HZAU), Wuhan

biorxiv.org/content/10.110… 2/ The novel coronavirus (CoV) is most closely related to merbocovirus HKU4. Merbecoviruses are betacoronaviruses that include MERS-CoV, HKU4-CoV and HKU5-CoV, from bats. We term the novel CoV 'HKU4r-HZAU-2020' to reflect its phylogenetic affinity, place and date of sequencing
Nov 30, 2022 • 30 tweets • 10 min read
Bat Forensics !! 🦇

Horseshoe bats are likely the ultimate reservoir of the ancestor of SARS2. Here I take a closer look at the Rhinolophus bat species present in the Mojiang mine, and discover two potentially new species/subspecies – with implications for the ID of RaTG13 2/ What is the reason for studying these bat species relationships ? Well, RaTG13 and RaTG15 were both isolated from the Mojiang mine, and both were described as being sampled from Rhinolophus affinis, the intermediate horseshoe bat 👇
Nov 21, 2022 • 10 tweets • 3 min read
Michael, I'd be pleased to do a whirlwind tour of the iconic RaTG13 and why the clade 7896 viruses might hold the key to its true identity RaTG13 is the closest related genome to SARS2 and was published early in the pandemic by the Wuhan Institute of Virology (WIV). A major difference between the two viruses is that SARS2 has a furin cleavage site (FCS), critical for its pandemic potential
Nov 21, 2022 • 18 tweets • 8 min read
Low levels of bacteria in the 'rectal swabs' used to generate 7896 clade sarbecovirus genomes 🧵

On the trail of the true identity of RaTG13 I decided to look at the 7876 clade NGS datasets (which include RaTG15), as these were also generated from the Mojiang mine.... Image 2/ RaTG13 has become iconic in the C19 Origins debate because phylogenomically it is the closest relative of SARS2, but there are anomalies and opacity in its history and sequencing
researchgate.net/publication/35…