Thread by @Ayjchan

On the recent paper describing new SARS2-like viruses in Thailand, the big takeaways for me:

The closest relatives to SARS2 are still from inside China whether you count it by genome, RdRp, or Spike RBD.

The ones from Thailand don't use human ACE2.

nature.com/articles/s4146…

I think sampling bats for viruses is worthwhile as long as care is taken not to introduce SARS2 from human personnel into wildlife while going on these expeditions.

BUT I don't think that hunting for bat CoVs in SE Asia is going to answer how this pandemic got started in Wuhan.

You're just going further and further away from ground zero. Wuhan (top dot), Kunming, Yunnan, China (middle dot) where the Mojiang miners and RaTG13 was collected, and Chachoengsao, Thailand (bottom dot) where the new bat CoVs were collected.

The origins story for how a bat SARS2-like virus endemic to South China (especially Yunnan) gets to Wuhan is already fanciful enough, often requiring a high speed train where no one else is infected during the transit, stopping off at different cities.

How does a bat SARS2-like virus from SE Asia get to China? This is the new tale that China really likes, and the WHO origins team has unfortunately said they're going to investigate in the next phase - switching from Proximal Origins in China to #PopsicleOrigins in SE Asia.

Essentially, because there's no external access to human or animal samples near Wuhan (top dot) or near Kunming (middle dot) where the closest relatives to SARS2 were found, now the investigation is going way down South to look for SARS2 viruses.

Never mind that no pangolins out of hundreds in Malaysia were found with CoVs. link.springer.com/article/10.100…

Never mind that none of the people closely handling the sick GD pangolins got infected.
conbio.onlinelibrary.wiley.com/doi/epdf/10.11…

Never mind that there are serious issues with the 2 #pangolinpapers that produced the pangolin CoV genomes with the SARS2-like Spike RBD... biorxiv.org/content/10.110…

We're riding the #pangolinexpress straight to Southeast Asia.

Also noticed something interesting when looking at the read coverage over the genome (particularly the Spike gene) of the Thai CoVs (Supp Fig 1). I don't know how to interpret this... why across 5 samples there is a dip in read coverage over the S1 of the Spike.

The Sanger sequencing read quality for RmYN02 over this region is also very interesting and I wish that the authors would've made those data available for other scientists to look at.

I don't know why some scientists are confident that looking for SARS2-like viruses in SE Asia over the next decades will help us find the #originsofcovid

Without access to human and animal samples in China, you have a major obstacle to the biodiversity arm of the investigation.

I could be wrong. I just think that searching around in SE Asia or parts of Europe for the #originsofcovid, instead of trying to get access to where it all started, seems like a fool's errand.