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Adrian J Profile picture
Adrian J
@humblesci
Bioinformatics and data science
Ava Profile picture 1 subscribed
Jul 26, 2023 • 4 tweets • 2 min read
Ben Hu research project Jan 2019- Dec 2021: "Pathogenicity of two new SARS-related coronaviruses to transgenic mice expressing human ACE2"

Ben Hu to @sciencemagazine "my work in the lab was mainly genome characterization and evolutionary analysis of viruses" Image h/t @Daoyu15 Image
Jul 1, 2023 • 8 tweets • 3 min read
First i'd like to thank Bob Garry, @acritschristoph and @jwgale for reading our preprint To address your comments: "the authors concluded "(a) the pangolin covs are actually from mice (b) actually, they were actually cloned artificial constructs, (c) actually, there were other viruses in the samples as well (d) actually, its all contaminated with dog dna""
Jun 21, 2023 • 18 tweets • 7 min read
Our preprint documenting a novel merbecovirus discovery in Guangdong is out on @biorxivpreprint

”Identification of a novel HKU4-related coronavirus in single-cell datasets and clade viral host analysis”

biorxiv.org/content/10.110… Image We identified a novel HKU4-reated coronavirus (CoV) "HKU4r-BGI-2020" in 7 pangolin single cell RNA-Seq datasets sequenced by BGI-Shenzhen in 2020. Image
Mar 15, 2023 • 10 tweets • 3 min read
No I wasnt aware of this, Hotez outsourced chimeric SARSr-CoV construction to the WIV as per this Zeng et al. 2017 paper

pubmed.ncbi.nlm.nih.gov/29134417/

under NIH grant R01AI098775 "a
recombinant virus (rWIV1-SHC014S) was constructed
based on the WIV1 backbone with the replacement of
SHC014S gene, as described previously (Zeng et al., 2016)"
Feb 21, 2023 • 8 tweets • 3 min read
Sorry, personally, I can't take Prof. Holmes public statements on origin of SARS-CoV-2 seriously after 1: stating publicly in a Jan 31 2019 article that the CoV likely spilled.over from animals at a Wuhan market, Then on Feb 1 in private stating the genome is inconsistent with evolutionary theory, and again in private on Feb 4 being 60/40 in favour of lab origin.

science.org/content/articl… Image
Feb 20, 2023 • 7 tweets • 3 min read
Newly discovered HKU4-related CoV, identified contaminating rice sequencing datasets in Wuhan.

biorxiv.org/content/10.110… The novel HKU4r-CoV has a 98.4% identity with nearest known CoV, BtTp GX2012, and c. 98% identities to HKU4 CZ07 and CZ01. Main differences to known HKU4r-CoVs is in the spike, ORF3a&b
Dec 12, 2022 • 14 tweets • 2 min read
Is Fauci the devil incarnate:

No

Does the possibility of an accident at a Wuhan virology lab conducting GOF research on SARS-related viruses need serious consideration and investigation?

Yes Is there dispositive evidence (or indeed any evidence) that SARS-CoV-2 jumped from animals at the Huanan Seafood Market?

No

Were there even any animals in any market in Wuhan that were found to be carrying a SARS-CoV-2 progenitor virus?

No
Dec 5, 2022 • 19 tweets • 3 min read
Raina MacIntyre on history of lab accidents and origin of SARS-CoV-2 -> we can't keep letting scientists with COI's controll the narrative if we want to prevent future pandemics

abc.net.au/radionational/… Listen from 16:30 here podcasts.apple.com/au/podcast/ome…
Oct 19, 2022 • 22 tweets • 6 min read
Huanan market zoonosis critique
Part 2: Environmental risk maps

Worobey et al. show in Fig. 4B of their recent Science paper a 'relative risk analysis of positive environmental samples' They write "We used a spatial relative risk analysis to
identify potential regions of the market with an increased density of positive environmental
samples. We found evidence (P < 0.05) of
a region in the southwest area of the market
where live mammals were for sale"
Oct 16, 2022 • 5 tweets • 2 min read
5 recent preprints challenging the Huanan Seafood Market origin hypothesis

1) Circular arguments on the origin of SARS-CoV-2 by @DavidBahry

zenodo.org/record/7016124 2) Statistical challenges for inferring multiple SARS-CoV-2 spillovers with early outbreak phylodynamics by @WashburneAlex et al

biorxiv.org/content/10.110…
Oct 9, 2022 • 21 tweets • 5 min read
Happy (and a bit relieved) to announce that our analysis of the zoonosis hypothesis at the Huanan Seafood Market (HSM) is online at Zendo.

zenodo.org/record/7169296 We undertake spatial analysis of COVID-19 cases at the HSM and find that the location of COVID-19 infections at the market follow a Poisson point process model and do not indicate spread from a single point source.
Aug 22, 2022 • 18 tweets • 5 min read
I'd like to respond to a critique by @niemasd 1) The focus of our paper is on the methods and assumptions used by Pekar et al. (2022) to rule out C/C and T/T intermediate genomes as true intermediates and by this conclude that intermediate genomes did not exist in humans.

Jul 24, 2022 • 11 tweets • 4 min read
Two pangolin SRA datasets AK706 (SRR11119760) and GE09 (SRR11119761) were deleted from NCBI on the 10/3/2020 but later released over a year later on the 16/6/2021 as noted by @sai_suryan usrtk.org/tag/pangolin-p… These were sequenced on the same machine and run number as sample M1 (@A00129 run 562), indicating AK706 and GE09 may not have been re-seqenced. What would be useful to find out is if AK706 and/or GE09 were modified after they were removed from NCBI and then re-released
Jul 23, 2022 • 25 tweets • 4 min read
"However, for much of the first year of the COVID-19 pandemic the scientific consensus favored a zoonotic explanation and concerns about the so-called lab escape theory were voiced mainly outside scientific circles. " ->any scientist who dared go against the narrative set by Calisher et al. & Andersen et al. was harrased, bullied and labelled a conspiracy theorists by fellow scientists, science journalists and media, firthermore any paper merely mentioning the possibility of a LL was rejected.
Jul 12, 2022 • 5 tweets • 2 min read
My co-authors @stevenemassey @Daoyu15 @ydeigin @quay_dr and I have just published another #pangolin CoV preprint. We review pangolin fecal samples DG14 and DG18 and find GD PCoV read distribution consistent with contamination by PCR targeted seqs.

arxiv.org/abs/2207.03288 In samples DG14 and DG18 we plasmid sequences containing Sus scrofa CD163 and a lager plasmid sequence containing SP6 RNA polymerase. Both of these plasmids have far higher read mappings than the GD PCoV in the dataset.
Jul 11, 2022 • 8 tweets • 4 min read
Our analysis of a novel SARS2r-CoV identified in game animal datasets in China shows the CoV to be related to GX #pangolin CoV and bat-SL-CoVZC45 in different sections of the partial genome researchsquare.com/article/rs-183… We found the novel CoV phylogeneticly groups with GX PCoVs in the NSP4, NSP10 and a 297nt section of the RdRp coding regions. NSP4:
Jun 26, 2022 • 9 tweets • 2 min read
Engineering CoVs using reverse genetics has been steadily advancing for the last 20 years. Its interesting, publishable work. pubmed.ncbi.nlm.nih.gov/32711735/ I can understand that you would be really annoyed if some group were working on a full length infectious clone, messed up and a lab worker got infected and infected others outside the lab.
Jun 25, 2022 • 4 tweets • 1 min read
Another way to think about SARS-CoV-2 origin scenarios is with a risk analysis decision tree Taking a (realistically) conservative estimate of 10% probability of a Wuhan virology lab accident while conducting research on a SARS-CoV-2 projenitor virus, we can use a decision tree (usually used before know outcome, here we dont know the mechanism)
May 11, 2022 • 21 tweets • 5 min read
Two insightful articles from Jan 2020. 26th @sciencecohen : "The virus came into that marketplace before it came out of that marketplace," Daniel Lucey asserts. Jan 31st "Ebright tells ScienceInsider that the 2019-nCoV data are "consistent with entry into the human population as either a natural accident or a laboratory accident." science.org/content/articl…
May 10, 2022 • 13 tweets • 4 min read
How EHA managed to bypass the pause on potential pathogen GOF research by rewording the monitoring clause, outsourced to Wuhan, breached terms on mulitiple occasions and has not subpoenad yet is beyond me (has not been subpoenad yet), but only a matter of time medium.com/@leftback45/pe…
May 8, 2022 • 4 tweets • 2 min read
Independent scientists proposing valid hypotheses or towing with party line: "Given the finding of SARS-CoV-2 on the surface of imported food packages, contact with contaminated uncooked food could be an important source of SARS-CoV-2 transmission" "Recently, SARS-CoV-2 antibodies were found in human serum samples taken outside of China before the COVID-19 outbreak was detected, which suggests that SARS-CoV-2 existed for some time before the first cases were described in Wuhan." science.org/doi/10.1126/sc…