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Adrian J

@humblesci

Oct 19

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"

@MichaelWorobey

@MichaelWorobey et al. discuss their analysis accounts for sampling biases and 'robustness' of the analysis to oversampling and overcounting. They conclude:
"In each case, the distance to live mammal vendors remained predictive of environmental sample positivity, "

Read 22 tweets

Adrian J

@humblesci

Oct 9

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.

Using Ripleys L function, (linearized K) analyzing the expected points within a distance r of a typical C19 case. Mean of random simulation=red dotted line. Observed distn. =black line. >>mean~clustering, <<mean~regular pattern. Clustering below 5m otherwise random distribution

Read 21 tweets

Adrian J

@humblesci

Aug 22

@niemasd

I'd like to respond to a critique by @niemasd

https://twitter.com/niemasd/status/1561525835084902400

https://twitter.com/stevenemassey/status/1560297573855920128

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.

https://twitter.com/stevenemassey/status/1560297573855920128

2) One of the 20 excluded genomes had SRA data available - we reviewed this Singapore genome excluded by Pekar et al due to 'low read depth', and using minimum read depth of 5X (virological.org/t/issues-with-…) conclude this is a likely T/T intermediate.

Read 18 tweets

Adrian J

@humblesci

Jul 24

@sai_suryan

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…

https://twitter.com/stevenemassey/status/1550853320704774149

@A00129

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

The interesting thing about sample M1 is that the GD_1 PCoV reads form a circular pattern, which we interpret to be related to molecular cloning arxiv.org/abs/2108.08163

Read 11 tweets

Adrian J

@humblesci

Jul 23

https://twitter.com/MJnanostretch/status/1550595495164350465

"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. "

https://twitter.com/MJnanostretch/status/1550595495164350465

->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.

"In an earlier essay on the potential effects of the COVID-19 pandemic for gain-of-function research, we too noted that in mid-2020 the idea of a lab origin for SARS-CoV-2 was more akin to a conspiracy theory than to an accepted consideration among scientists,

Read 25 tweets

Adrian J

@humblesci

Jul 12

@stevenemassey

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.

We also add to our previous analysis of GX PCoV sample GX/P3B and find numerous cloning vectors in the dataset and human genomic content.

Read 5 tweets

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