Authors Francisco de Asis

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Francisco de Asis
Francisco de Asis
@franciscodeasis
[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

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

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
https://t.co/Mf0AeRatge
https://t.co/C444TLT6JO


LiBiao Zhang was probably in the mine on 27-Jul-12 with HKU team (he is co-author in Lau et al. (2017)) and a week later on 06-Aug-12 with WIV in their 1st visit. Surprisingly, he is co-author in the AdV isolates paper, but not credited in Ge et al. (2016)
https://t.co/ZNW6sd976T


LiBiao Zhang was also sampling in the same location as Holmes. GPS coordinates are 4 km apart, although it seems that Holmes’ team obfuscated a bit the location. He may even have sampled a close relative bat unnoticing that was infected with similar
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Francisco de Asis
Francisco de Asis
@franciscodeasis
@luigi_warren @BahulikarRahul @Daoyu15 @AntGDuarte @babarlelephant @TheSeeker268 @BillyBostickson @PaulGodolphin @BioObject @JJ2000426 @Nomdeplumi1 @_coltseavers @scottburke777 @still_a_nerd @jjcouey @Harvard2H @ydeigin @uacjess @CarltheChippy @DefeatTheElites @ico_dna @Real_Adam_B @nerdhaspower @RolandBakerIII @DrAntoniSerraT1 @babarelephant 中华菊头蝠 --> Rhinolophus sinicus (Rs)
You can also see that in the abstract written in English. At that time they think that SARS came from Rs. Although Shi eventually obtained their first (declared) SARS-like in a Ra in their 4th and last trip (known).

@BahulikarRahul @Daoyu15 @AntGDuarte @babarlelephant @TheSeeker268 @BillyBostickson @PaulGodolphin @BioObject @JJ2000426 @Nomdeplumi1 @_coltseavers @scottburke777 @still_a_nerd @jjcouey @Harvard2H @ydeigin @uacjess @CarltheChippy @DefeatTheElites @ico_dna @Real_Adam_B @nerdhaspower @RolandBakerIII @DrAntoniSerraT1 @babarelephant From the MSc dissertation of Li Xu published in May-13.
The outbreak started in April, the miners went to hospital at the end of April and first days of May.
3 deaths: May, Jun & Aug (so, that could be the reason that early news stated only two deaths). RIP


@BahulikarRahul @Daoyu15 @AntGDuarte @babarlelephant @TheSeeker268 @BillyBostickson @PaulGodolphin @BioObject @JJ2000426 @Nomdeplumi1 @_coltseavers @scottburke777 @still_a_nerd @jjcouey @Harvard2H @ydeigin @uacjess @CarltheChippy @ico_dna @Real_Adam_B @nerdhaspower @RolandBakerIII @DrAntoniSerraT1 @babarelephant Here an updated version with some additions. Thanks @gdemaneuf for finding new info and a typo.
- Li's admission date seems incorrect (generates discrepancies). Probably was around 30-Apr-12
- There were two different groups
- Each group member had the first CT the same day


@BahulikarRahul @Daoyu15 @AntGDuarte @babarlelephant @TheSeeker268 @BillyBostickson @PaulGodolphin @BioObject @JJ2000426 @Nomdeplumi1 @_coltseavers @scottburke777 @still_a_nerd @jjcouey @Harvard2H @ydeigin @uacjess @CarltheChippy @ico_dna @Real_Adam_B @nerdhaspower @RolandBakerIII @DrAntoniSerraT1 @babarelephant @gdemaneuf Some observations: Lu's 1st symptoms date is approx. ("half a month ago"), so for the first 4 miners the 1st symptoms date is quite the same, suggesting simultaneous zoonotic events and no h2h. But for the other 2 miners it was earlier than the others (4.5 vs 11.25 days). h2h?

@BahulikarRahul @Daoyu15 @AntGDuarte @babarlelephant @TheSeeker268 @BillyBostickson @PaulGodolphin @BioObject @JJ2000426 @Nomdeplumi1 @_coltseavers @scottburke777 @still_a_nerd @jjcouey @Harvard2H @ydeigin @uacjess @CarltheChippy @ico_dna @Real_Adam_B @nerdhaspower @RolandBakerIII @DrAntoniSerraT1 @babarelephant @gdemaneuf There were two work shifts: 1. April 2nd to 16th; 2. April 22nd to 26th.
Maybe the leader of the 1st group met the 2 other miners to explain the work and infected them (h2h), or maybe the 1st group were only exposed to the virus in the last 4-5 days (no h2h)
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Francisco de Asis
Francisco de Asis
@franciscodeasis
[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


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

I always make this assumption: WIV ability of faking sequences is not unrestricted. They would never fake aa seqs, due to the protein folding problem. In a few months or years, they would be

So, in silico, WIV would never make:
- non-synonymous mutations
- splicing within genes
But they could make:
- synonymous mutations
- swap genes or the complete genome from other real viruses
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Francisco de Asis
Francisco de Asis
@franciscodeasis
[Thread] Wang et al. (2021):
Another article revealing trips to the Mojiang mine and Laos was kept in the limbo when the pandemic started.
Note: The article covers HKU10 viruses which are not related with SARS-like

It was "received" by the journal on 30 July 2021, but the sequences were accessioned in Genbank on 17-SEP-2019.
So it seems that this article may have prior rejections or have been withdrawn from other journals.
https://t.co/laNmTabCuk


One of the samples is 4996 (note that RaTG13 = 4991).
There is a small discrepancy: 4991 was collected on 24-Jul-13 but this one on 21-Jul-13.
4996 is 100% identical to MJ_67C (from HKU team when they went to Mojiang) and clusters with 3723 (Mojiang).
https://t.co/XqMEyEi45T


Btw, 3740 (Mojiang) and 7345 also cluster together, supporting that 7345 is from Tongguan/Mojiang as we already deduced a year


The article does not explicitly say they collected samples from Mojiang, although the low-res map confirms it.
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