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19 Apr, 7 tweets, 2 min read
[Thread] Missing / unpublished sequences
WANTED: Live isolates WIV15 & WIV6; Ra7896 (complete genome); EPI_ISL_402122; MT394201
Two live isolates missing. Serious issue!
WIV6 and WIV15
We need full disclosure of Ra7896 & clade. NOW!
Why a gap in this series?
What happened with EPI_ISL_402122?
Why IVDC-HB-02 & IVDC-HB-03 missing?
NCBI cannot release this Accession which probably contains an ACE2 seq. It should by done by the authors. Waiting since summer 2020. Release it now!
Some other unpublished viruses
Oops, errata:
I mean MT394202, not MT394201
The link inside the tweet was correct:
ncbi.nlm.nih.gov/nuccore/MT3942…

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More from @franciscodeasis

Francisco de Asis Profile picture
16 Apr
[Thread] In-silico molecular overclocking of RaTG13.
TLDR: 191-nt RdRp segments of SARS-CoV-2, RaTG13 and Ra7896 show an unexpected molecular clock behavior. In-silico synonym mutations is one probable explanation.
Assuming SARS-CoV-2 is an ancestor of Ra7896 (used in RaTG13) does not fully explain it. Implied evolutionary rate would be in the order of 10^-2 substitutions/site/year in a well-conserved part of the genome, far from a normal ~10^-3 for a complete genome
So, it is not only SARS-CoV-2 having its molecular clock frozen, but also RaTG13 molecular clock running more than expected.
@Nerdhaspower and @Quay_Dr have already noted strange patterns of synonym mutations along the genome of RaTG13
Read 10 tweets
Francisco de Asis Profile picture
18 Mar
@MonaRahalkar @Daoyu15 @babarlelephant @Drinkwater5Reed @idomyownexpts @AntGDuarte @Rossana38510044 @jhouse678 @daoyu But we would know a few things:
- ancestor of Ra7896, so, before May-15
- very close to Ra4991, but not Ra4991 (has 5 mutations in 370)
- not the miner's virus
It could be what you mentioned long time ago: other samples. But not initially hidden, but detected very late. Maybe
@MonaRahalkar @Daoyu15 @babarlelephant @Drinkwater5Reed @idomyownexpts @AntGDuarte @Rossana38510044 @jhouse678 @daoyu OTOH, the RBD should come from the mine too. We already know there was one there in April 2012. They eventually found a descendant
@MonaRahalkar @Daoyu15 @babarlelephant @Drinkwater5Reed @idomyownexpts @AntGDuarte @Rossana38510044 @jhouse678 @daoyu A good candidate for WIV15 could be 1 of the 43 samples of Ra from the 3rd trip in April 2013
Read 14 tweets
Francisco de Asis Profile picture
4 Mar
[Thread of threads] #originsofSARSCoV2 #DRASTIC
Compilation of relevant findings. Live thread.
Let's start with the Addendum and the 7896 clade recently confirmed to come from the Mojiang mineshaft
Read 14 tweets
Francisco de Asis Profile picture
14 Feb
[Thread] Pangolin CoV... or Bat CoV in pangolins samples?
TLDR: A researcher of the team that sequenced the pangolins samples had taken samples in the mine of RaTG13 and in the place where RmYN02 was collected, also catched bats in Yunnan. Probably contaminated pangolin samples
@Daoyu15 was the first to note that the raw sequence reads of the pangolins “contained unexpected reads and was in serious risk of contamination” in early June 2020. But now we can explain how it was possible to happen this in Guangdong
zenodo.org/record/4450267…
Jin-Ping Chen, the corresponding author of the first paper of the pangolins, and LiBiao Zhang, who has been sampling the mine of RaTG13 and the place in Mengla where RmYN02 was collected, are close colleagues in GIABR & GIZ
ncbi.nlm.nih.gov/pmc/articles/P…
giz.gd.cn/yjdw_/yjy/
Read 10 tweets
Francisco de Asis Profile picture
14 Feb
[Thread] Unnoticed Lab contamination in the samples of first COVID-19 infected patients.
1/ Article: “There was a simultaneous undetected outbreak of Nipah in Wuhan”

Explanation:
2/ Article: “Non-SARS-CoV-2 genome sequences identified in clinical samples from COVID-19 infected patients”
peerj.com/articles/10246/

Explanation:
3/ Pre-print: “adenovirus infections” in first patients

Explanation:
Read 4 tweets
Francisco de Asis Profile picture
4 Feb
@TheSeeker268 @Daoyu15 @Undergroundsar3 @Real_Adam_B @BillyBostickson @Rossana38510044 @luigi_warren @babarlelephant @AntGDuarte @MonaRahalkar @flavinkins @KevinMcH3 @DrAntoniSerraT1 @_coltseavers @rowanjacobsen @uacjess @RolandBakerIII @still_a_nerd @jjcouey @Harvard2H @ydeigin @CarltheChippy @ico_dna @nerdhaspower @scottburke777 @JJ2000426 @BahulikarRahul @alimhaider @antonioregalado @Ayjchan @R_H_Ebright @BretWeinstein @sanchak74 @JCalvertST @PeterDaszak @TheSeeker @nature @threadreaderapp
@TheSeeker268 @Daoyu15 @Undergroundsar3 @Real_Adam_B @BillyBostickson @Rossana38510044 @luigi_warren @babarlelephant @AntGDuarte @MonaRahalkar @flavinkins @KevinMcH3 @DrAntoniSerraT1 @_coltseavers @rowanjacobsen @uacjess @RolandBakerIII @still_a_nerd @jjcouey @Harvard2H @ydeigin @CarltheChippy @ico_dna @nerdhaspower @scottburke777 @JJ2000426 @BahulikarRahul @alimhaider @antonioregalado @Ayjchan @R_H_Ebright @BretWeinstein @sanchak74 @JCalvertST @PeterDaszak @TheSeeker @nature @threadreaderapp This email seems to be an automatic email upon submission. It is dated as Jan 8th consistent with what the Genbank ID method suggests (Note: allow 1 day of difference due to timezones or slow batch processes). So, what is the other date of Jan 5th?
@TheSeeker268 @Daoyu15 @Undergroundsar3 @Real_Adam_B @BillyBostickson @Rossana38510044 @luigi_warren @babarlelephant @AntGDuarte @MonaRahalkar @flavinkins @KevinMcH3 @DrAntoniSerraT1 @_coltseavers @rowanjacobsen @uacjess @RolandBakerIII @still_a_nerd @jjcouey @Harvard2H @ydeigin @CarltheChippy @ico_dna @nerdhaspower @scottburke777 @JJ2000426 @BahulikarRahul @antonioregalado @Ayjchan @R_H_Ebright @BretWeinstein @sanchak74 @JCalvertST @PeterDaszak @TheSeeker @nature @threadreaderapp Could be this:
"GenBank will provide accession numbers for submitted sequences, usually within two working days"
NCBI still has many non automated processes, even receiving submissions by email. So that could explain those 3 days of difference
ncbi.nlm.nih.gov/genbank/submit/ Image
Read 12 tweets

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