[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.

https://twitter.com/franciscodeasis/status/1371636663064137729

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

https://twitter.com/franciscodeasis/status/1371636663064137729

@Nerdhaspower

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

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Francisco de Asis

@franciscodeasis

18 Mar

@MonaRahalkar

@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

@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

@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

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Francisco de Asis

@franciscodeasis

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

@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

@franciscodeasis

14 Feb

https://twitter.com/sanchak74/status/1311349657193254913

[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”