1. While awaiting @shingheizhan reassembling of RaTG13, here's a thread with some odd features reported by authors who made use of its GenBank sequence. Most of them used the sequence for other research goals, rather than assessing it, so its anomalies are mentioned incidentally.
2. This Feb 2020 preprint found that synonymous mutations "are dramatically elevated between SARS-CoV-2 and RaTG13" and "enriched in T:C transition."
Since some RNA mutagens "could induce the same mutation pattern", authors suggest further investigation.
biorxiv.org/content/10.110…
Since some RNA mutagens "could induce the same mutation pattern", authors suggest further investigation.
biorxiv.org/content/10.110…
3. @Nerdhaspower's was the first paper I read raising doubts about RaTG13 sequence.
Issue: two bat CoVs show nonsyn mutations evenly distributed along their S sequences. For RaTG13 vs SARS-CoV-2 they appear heavily concentrated around codons 300-500. Why?
nerdhaspower.weebly.com/ratg13-is-fake…
Issue: two bat CoVs show nonsyn mutations evenly distributed along their S sequences. For RaTG13 vs SARS-CoV-2 they appear heavily concentrated around codons 300-500. Why?
nerdhaspower.weebly.com/ratg13-is-fake…
4. Since RaTG13 is available only as a GenBank sequence, its spike has been synthesized accordingly in order to be tested.
A study found this synthetic spike showing a surprisingly low affinity for usually tested ACE2, and for bat ACE2 in particular. biorxiv.org/content/10.110…
A study found this synthetic spike showing a surprisingly low affinity for usually tested ACE2, and for bat ACE2 in particular. biorxiv.org/content/10.110…
5. RaTG13 was found in a R. affinis bat, a crucial species for SARS virus genealogy. Yet, despite the sampling of 100s of these bats in China, its ACE2 sequence is unknown. Question: why does RaTG13 spike show so little affinity for other Rhinolophus ACE2? biorxiv.org/content/10.110…
6. @ras_nielsen preprint looked deep into syn mutations of RaTG13 and SARS-CoV-2, also considering the recently reported RmYN02 sequence. Issue: RaTG13 (allegedly sampled in 2013) shows same molecular clock dating as the other two viruses sampled in 2019. biorxiv.org/content/10.110…
7. These authors synthesized RaTG13 spike and compared it with the spike of SARS-CoV-2 using cryo-EM.
They report that RaTG13 spike protein was found to be so unstable that it required extensive "optimization and cross-linking" in order to be micrographed. nature.com/articles/s4159…
They report that RaTG13 spike protein was found to be so unstable that it required extensive "optimization and cross-linking" in order to be micrographed. nature.com/articles/s4159…
8. A recent study by @Scinquisitor "found a 9-fold excess of G–U transversions among SARS-CoV-2 mutations over relative substitution frequencies between SARS-CoV-2 and (...) RaTG13".
This comparison was much lower for SARS-CoV and non-existent for HKU1.
peerj.com/articles/9648/
This comparison was much lower for SARS-CoV and non-existent for HKU1.
peerj.com/articles/9648/
9. Phylogenetic Bayesian analyses have variably estimated the TMRCA of RaTG13 and SARS-CoV-2 anywhere from 20 to 70 years.
Based on a protein metric, MeaPED, @some_wise estimates they split in 2012.
Another sign of dN/dS artifacts in RaTG13 sequence?
osf.io/ntc8w
Based on a protein metric, MeaPED, @some_wise estimates they split in 2012.
Another sign of dN/dS artifacts in RaTG13 sequence?
osf.io/ntc8w
10. These aspects of RaTG13, and many other Covid-related ones, have been analysed (at times, discovered) over many hours of work by some amazing people on a Twitter group that I'm proud to be part of. Many thanks, extended to all others who engage & work in the pursuit of truth.
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