So, this excellent preprint came out a few hours ago and I have to say we’re getting closer to understanding where SARS-CoV-2 came from and where similar pandemic CoVs might be! researchsquare.com/article/rs-871… 🧵⬇⬇
Got home and gave it a proper read (i.e. stared at the supplementary phylogenies) and here are some interesting bits below: (I’m gonna go through the trees for some non-recombinant fragments, so fig2 here is helpful) 
The fragment 3 tree is important, cause for this region BANAL103 and 52 seem veery close to SARS-CoV-2. This genome bit is probably the evolutionarily closest relative to SARS-CoV-2 to date. (need to run some dating once the seqs are out).
Also, the bat species are the usual culprits: R. pusillus (RpYN06) – w/ a wide host range & R. malayanus (RmYN02) w/ a range connecting the Indochinese peninsula to China through Yunnan.
“Interestingly, one should note that very similar SARS-CoV-2-like viruses are shared by different bat species, suggesting a possible circulation of viruses between different species living sympatrically in the same caves” – v well put by the authors!
Moving on, fragment 4 tree shows all 5 new viruses clustering closely with the RmYN02/PrC31/RpYN06 cluster sampled in Yunnan, i.e. all these viruses recently shared a common host population (bats) that moved (flew?) from one place to the other.
The pattern becomes even more intricate in fragments 10&11 where only 2 viruses share the non-SC2-like recombinant bit that RmYN02 also has.
This means that either recombination happened right after divergence of the viruses or (more likely) the recombinant bit in the other viruses got ‘overprinted’ by more recombination! Either way this suggests A LOT of opportunity for recombination btn CoVs in bats!
We talk about recombination patterns and overprinting in our preprint here if you wanna read more: biorxiv.org/content/10.110…
Oh and last thing the fragment 10 tree shows the BANAL103 and 236 clustering with the Guangdong pangolin CoV, supporting the hypothesis that pangolins get the CoVs from independent jumps from bats.
My key takeaways:
1️⃣ these viruses can quickly move through wide geographic ranges on their bat reservoir hosts
2️⃣ there's more recombination opportunities than we think
3️⃣ apart from more virus sampling we need a thorough map of horseshoe bat movement routes!
1️⃣ these viruses can quickly move through wide geographic ranges on their bat reservoir hosts
2️⃣ there's more recombination opportunities than we think
3️⃣ apart from more virus sampling we need a thorough map of horseshoe bat movement routes!
great work to all the authors involved, this is a very well presented manuscript!
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