Evolutionary Virologist at the @SystemsVirology lab, University of Tokyo 🇯🇵
Molecular Evolution, Phylogenetics, Viral Genomics
(he/him)
💻🔬🏳️🌈
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Apr 6 • 6 tweets • 2 min read
Some thoughts on the H5N1 situation 🦆🐄🦠 First, the situation is very concerning. this virus does not trasmit h2h, but the more animals in close contact with humans it infects the more the chance of h2h becoming a possibility. Now onto the interesting mutations:
We have shown that viruses with NP:Y52H can evade BTN3A3, a human antiviral gene against avian flu (). This mutation happens quite frequently in avian viruses.nature.com/articles/s4158…
Nov 29, 2023 • 13 tweets • 4 min read
🚨New paper alert! and it's one I'm really excited for! Resurrection of OAS1 from the ancestor of modern horseshoe bats blocks SARS-CoV-2 replication now out in @PLOSBiology
Here's a 🧵on how we reconstructed an ancient 🦇anti-CoV protein
doi.org/10.1371/journa…
Animals have many diverse mechanisms to restrict viral infection, some maintained for millions of years and others lost at certain points in time. In this paper we use computational and experimental approaches to go back in time in the evolution of the horseshoe bat OAS1 gene.
Jul 6, 2023 • 15 tweets • 3 min read
I promised some thoughts on avian H5s based on our recent results and I've decided to link these up to the current H5N1 cat outbreak in Poland. Long story short, oneoff cat to human infections should be a worry, but onward h2h transmission is unlikely with the current situation.
In our recent paper we found a human-specific inhibitor of avian IAV infection (BTN3A3) which can be evaded by a single aa substitution in either of 2 sites on the viral NP
It's finally out! an exciting paper almost 4 years in the making: BTN3A3 evasion promotes the zoonotic potential of influenza A viruses in @Nature Here's a 🧵 about how 🐓 influenza A viruses cross the species barrier nature.com/articles/s4158…
the work, spearheaded by our flu aficionado @RuteMPinto started off with screening a number of ISGs (interferon-stimulated genes) with an array of pathogenic viruses, to see if expression of any of these genes stops virus replication
Wee🧵about our recent paper on the origins and virological characteristics of the SARS-CoV-2 XBB variant published last week in @NatureComms with G2P-Japan, @jampei2@SystemsVirology 🦠🧬 nature.com/articles/s4146…
Our previous paper on the BQ.1.1 variant let us understand the importance of convergence in the evolution of SC2. The emergence of XBB let us delve into a second crucial evolutionary process of SC2, recombination!
Recently I've been too busy to engage with the latest cuckoo discussions on SARS-CoV-2 origins, but I wanted to comment on the Senator Burr report that's making the rounds, especially since they use a figure I made (!) for their fig2 help.senate.gov/imo/media/doc/…
First things first, I was never consulted about this report or had any knowledge of it before the last 24 hours.
Feb 9, 2022 • 23 tweets • 9 min read
Now onto the technical bits! When viruses recombine with one another different segments of their genomes will have different evolutionary histories (since a recombinant bit used to technically be in a different virus before recombining into the one we're looking at)
That's why making a phylogeny based on a whole-genome alignment of recombinant viruses can be extremely misleading! Accounting for complex recombination patterns had already been deemed important in early analysis of SARS-CoV-2's pre-pandemic evolution: nature.com/articles/s4156…
Nov 23, 2021 • 6 tweets • 3 min read
In light of the re-sparked discussions about the SARS-CoV-2 furin cleavage site origin I wrote an update on my original @virological_org post (posted more than a year ago... how time flies...) A few points here: 🧵 virological.org/t/the-sarbecov…
Given the available sampling data, I think that the most likely origin of the FCS is copy-choice recombination from a yet unsampled RmYN02-like virus clade.
Sep 28, 2021 • 4 tweets • 2 min read
We got a new paper now published at @ScienceMagazine !! 🎉 The prenylated form of OAS1 can sense SARS-CoV-2 in humans and protect against severe COVID19!
paper here: science.org/doi/10.1126/sc…
+ thread here:
my favourite bit? the sequence responsible for prenylation has been lost in the horseshoe bat (Rhinolophoidea) OAS1 protein through an ancient retrotransposition event! This finding brings in new questions about how these CoVs interact w/ their reservoir bat hosts.
Sep 17, 2021 • 12 tweets • 4 min read
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)
Aug 30, 2021 • 14 tweets • 4 min read
Here are some extra twitter thoughts on our perspective on the likely origins of the COVID-19 pandemic recently published @ScienceMagazine - with Wei Xia, @blJOg , @john_jxw , @robertson_lab . 🧵⬇ science.sciencemag.org/content/373/65…
Despite the storm of opinions on and constant politicisation of the search for the origins of SARS-CoV-2, imho the science should really be focused on increasing our efforts for virus sampling and surveillance.
May 28, 2021 • 9 tweets • 3 min read
Preprint updated with a lot of exciting new analyses and data! biorxiv.org/content/10.110…
The world is going mad about the origins of SARS-CoV-2, so we did some cool recombination analysis and phylogenetics! I'll briefly explain the key takeaway points below (mini-🧵):
We find ample evidence of recombination across the evo history of SARS-related viruses. We determined the clearest recombination breakpoints across these genomes and split the alignment into non-recombinant genome segments to make some trees.
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