Alina Chan Profile picture
18 Oct, 8 tweets, 3 min read
The RaTG13 genome was just quietly updated on Oct 13, 2020.

Why is this happening!?
ncbi.nlm.nih.gov/nuccore/MN9965…
I thought the sample disintegrated in 2018 after full sample sequencing was done (even though the Nature paper said it was sequenced post-COVID). What is there to update?!
Do scientists need to be assigned to just sit and watch these data depositions for RaTG13, pangolin CoVs, RmYN02 to see what new data accessibility or updates occur over the years?
Between the 2 versions, there are at least 4 single base changes, and 1 double base change that several scientists have already noticed.

It is October. Shouldn't a genome fully sequenced in 2018, published in January be accurate?
The only notice on the Nature paper that RaTG13 was first named in: "28 September 2020 This article was amended to correct the Peer review information."
nature.com/articles/s4158…
To be fair to the journals, I 100% don't believe that @Nature was notified about this change made by the authors to the data published in the journal. This is why changes to datasets and papers cannot keep going on unannounced. This means both the journal and readers are blinded.
Similar thing happened with the @Nature pangolin CoV paper. New sample pangolin_10 was just quietly added to the bioproject on June 22 (Xiao et al. paper published on May 7, 2020). This new sample doesn't match samples described in the paper. @shingheizhan ncbi.nlm.nih.gov/sra/SRX8582289
I don't know what to say about this in a way that is meaningful to a layperson. There are a lot of things wrong with research & the publishing process that are amplified by COVID. Maybe the best thing is to engage trusted journalists @sciencecohen to clear things up with the WIV.

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More from @Ayjchan

20 Oct
Very glad that the paper by @MonaRahalkar and @BahulikarRahul is finally published in a peer-reviewed journal. We need more scientists and journalists looking at possible links between SARS-CoV-2 origins and the 2012 Mojiang miners. frontiersin.org/articles/10.33…
I know of experts don't want to consider the miners because it is too far out of, frankly, anyone's field. But if experts don't look at the miners because it is outside their specialization, and journalists don't look at them because of the complex science, then who will?
Apparently, the answer is semi-anonymous users on twitter, who have recently named themselves DRASTIC (Decentralized Radical Autonomous Search Team Investigating COVID-19).

Their findings were described in the Sunday Times (still behind paywall) in July. thetimes.co.uk/article/seven-…
Read 5 tweets
14 Oct
"The Guangdong (pangolin CoV) strains, which were isolated or sequenced by different research groups from smuggled pangolins, have 99.8% sequence identity with each other."

I wonder how that could happen!

nature.com/articles/s4157…
Let me clear this up. The same senior authors have repeatedly published this -singular- batch of pangolin samples. Did they actually isolate the virus in culture? If so, why not share this with other researchers worldwide? See details here: biorxiv.org/content/10.110…
Read 25 tweets
13 Oct
COVID mink outbreaks: Netherlands (41+ farms), Denmark (63 farms), Spain, US (Utah, 9 farms; Wisconsin; Michigan)... we're going to have to add a host species feature to covidcg.org once sequences from mink SARS2 isolates are added to @GISAID. independent.co.uk/news/world/eur…
The only troubling part: "The (Danish) government says breeders with non-infected mink will be given 100 per cent compensation, while those with infected animals will receive less as an incentive for farmers to keep the infection out of their stock."
Wouldn't this incentivize farmers to hide mink outbreaks in their farms so that they can receive full compensation? Please reconsider this policy, Denmark!
Read 4 tweets
11 Oct
Read the 2nd Yan et al. report. It was frustrating... each statement requires fact-checking to the point where, instead of pointing out the errors, it may be better for someone to write an independent article discussing the circumstantial evidence pointing to lab origins.
The overarching message of Yan's 2nd report is that there has been unscientific behavior surrounding the reporting of SARS2-like CoVs. Based on this, they speculate that these genomes are coordinated fakes to make SARS2 look natural.
Again the report is littered with errors, but I do wonder why there hasn't been international impetus to investigate the source of these SARS2-like viruses. Why not go to the Yunnan mine to look for more RaTG13s? Why not investigate the miners - what actually happened in 2012?
Read 21 tweets
5 Oct
Beseeching employers in Canada to make work as remote as possible. If your employee is not, e.g., a healthcare worker, requiring in-person interaction, there is no reason why they should be out there at risk + increasing the risk for essential workers.
cbc.ca/news/canada/wo…
I wonder, often, at employers who think IT/admin people must be at the office. You can basically look South to see what happens when people treat this virus like it's not serious. Not everyone has access to (1) regular testing and (2) new therapeutics + a top class medical team.
The question at this point is how many deaths and disabilities your employer needs before they decide to make work remote. You already know cases are rising, that means many undetected cases. And you know people with pre-existing conditions have a fair chance of death/disability.
Read 8 tweets
30 Sep
Been hearing a lot about using Vitamin D to fight COVID. Finally got around to reading the paper that is at the root of all this.

tldr the science is far from settled, but, yes, it should be considered for -elderly- patients with Vitamin D deficiency.

sciencedirect.com/science/articl…
First things first, the form of vitamin D used in this study is not the nutritional vitamin D you can buy off the shelf. The authors say as much in the paper: "Our study does not include a comparison with cholecalciferol, the native vitamin D3 form"
2nd, although patients were selected at random, the authors clarify this study was NOT double-blind placebo controlled. What this means: the doctors/organizers (and the patients) knew who was or was not receiving calcifediol (prehormone produced by hydroxylation of vitamin D).
Read 17 tweets

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