Spyros Lytras
@SpyrosLytras
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Evolutionary Virologist at the @SystemsVirology lab, University of Tokyo 🇯🇵 Molecular Evolution, Phylogenetics, Viral Genomics (he/him) 💻🔬🏳️🌈
Tokyo, Japan
Joined March 2014
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Pinned Tweet
Very happy to have this one published in
@Nature
today!! 🤩🤩 Can we dig deeper into the intricate and ancient evolutionary history of the flaviviridae by comparing not only genetic sequence but also protein structure? answer is yes!!
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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
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Big news! Our perspective on the origins of SARS-CoV-2 is now out at
@ScienceMagazine
❗❗
Trading of animals susceptible to bat coronaviruses is the likely cause of the
#COVID19
pandemic, say
@SpyrosLytras
,
@robertson_lab
and colleagues in this
#SciencePerspective
.
Read more:
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Our paper on SARS-CoV-2 origins and recombination is finally published at GBE
@GenomeBiolEvol
@OfficialSMBE
!! Here's a lengthy 🧵 about bats 🦇, sarbecoviruses 🦠, recombination 🧬 and the origins of a nasty pandemic:
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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
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🚨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
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Preprint updated with a lot of exciting new analyses and data!
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-🧵):
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✨New title unlocked!!✨ Finally a Dr! Big thanks to
@katrina_lythgoe
and
@rbiek
for a great viva and ofc to my wonderful supervisors for the past four years
@blJOg
@SamJWilsonPhD
@robertson_lab
!! 😁😁🎉🎉
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As promised here is a summary 🧵 of our paper 'Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen' now published in
@PLOSBiology
1/18
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Guess who's finally a real virologist! Got my very first plaque assay today!! Thanks to an excellent mentor (and photographer 📸)
@MTurnbullCVR
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This paper is really cool! Highlights how different omicron is from the previous variants (and apparently all other SC2-related viruses!)
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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:
If I’m not wrong this sequence has NP:Y52H, a mutation which
@RuteMPinto
and
@SpyrosLytras
linked to immune evasion to BTN3A3, a restriction factor for human infection by avian influenzavirus.
…
@RajlabN
@PeacockFlu
@LongDesertTrain
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We got a new preprint up on
@biorxivpreprint
!! The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2 🦇🦠🗺
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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! 🧵⬇⬇
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It also provides no actual evidence for a lab origin of the virus (WIV just being in Wuhan is NOT real evidence of a lab leak) and contains plenty of political 'US vs China' discussion points (that imho obstruct the scientific search for the pandemic's origins).
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To my understanding this is a US senate commissioned report assessing the origins of SC2. Not sure who actually wrote it (don't really care), but they've done a very VERY bad job at reporting the science on this topic... here's some thoughts:
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We got a new preprint out! it presents a huge project that I've been part of since before the pandemic (sure feels like a long time 😬)
Zoonotic avian influenza viruses evade human BTN3A3 restriction, a 🧵
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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: 🧵
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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
. 🧵⬇
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1. The report seems to assume that my figure 2 phylogeny is the single way these viruses are related, but this isn't the case. this tree is derived from only one non-recombinant bit of the viruses' genomes.
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A very lovely welcome at the
@SystemsVirology
lab!! Let's do some cool science together!! 😁😁🎉🎉
Super happy to accept a Super Saiyan, also known as a super postdoc or Spyros
@SpyrosLytras
, to my lab. It was his day 0 as a postdoc in Japan🇯🇵. Welcome back. What a big day!!
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Wow... I don't engage with the usual cranks but I will call out influential people who've been covering COVID news when they're utterly wrong (and seemingly v confident about their misleading statements...)
@RottenInDenmark
There hasn’t been much evidence of any kind, either way, due to an extensive cover up. Acting like there is some direct evidence accumulating on one side is incorrect. What’s wrong with we don’t know? It’s factual.
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Finally found some time to put together my personal website, featuring what I do, papers, our cool animated video on how we study SARS-CoV-2 evolutionary history, and more!
Check it out!
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Glad to have contributed to this excellent article at
@ScienceMagazine
by
@sciencecohen
with some tree-making sparkle 🌲✨
Well worth a read to see the latest picture of SARS-CoV-2 relatives in the wild + discussion on surveillance VS virus discovery.
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All in all, this report cherry picks data and in many cases makes assertions that completely contradict the scientific facts and data that are available.
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great article on the new Laotian bat viruses and what this discovery means for the origins of SARS-CoV-2!
(Got my own quote in there too! 🙂)
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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:
+ thread here:
New
@wilsonlabcvr
paper. Our work, led by
@virologist_atu
, showing that the prenylated variant of OAS1 can sense SARS-CoV-2 and protect against severe
#COVID19
is out in Science:
#CVRCovidResponse
🧵 (with some new bits)
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Had a fantastic time at
#awaji2023
in Karuizawa 🇯🇵 this past week! Here's me presenting our recent paper on human BTN3A3 restricting avian IAV infection! Read the full paper in
@Nature
here:
@CVRinfo
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I mention this since we recently discovered that a single amino acid change at flu's NP protein can evade an important human-specific immune response and that change has happened in both 1918 and 2009 independently:
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In fact, the GBE paper shown at the bottom of fig2 (but not referenced or mentioned in the report's text) goes into great depth about how important recombination is and how every chunk of the viruses genomes has a very different evolutionary history:
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Guess the news are out! Can't thank enough everyone at
@CVRinfo
for the fantastic last 4 years! Cause apart from the fun science, I got to make some amazing friends ❤️ now off to a new adventure, wil be joining
@SystemsVirology
in gorgeous Tokyo this Jan!
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It was an honour representing the
@CVRinfo
@UofGlasgow
at the
@Els_Vaccine
17th Vaccine Congress, here in Glasgow! As a non-vaccinologist I got to learn a great lot about vaccines from all the other speakers!
#17VaccineCongress
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one example of many other large-scale zoonotic human pandemics being very 'well-adapted for human-to-human transmission' is the avian flu 1918 pandemic and swine flu 2009 pandemic...
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thesis corrections accepted (officially a Dr?), paper provisionally accepted, and new banging
@troyesivan
album! pretty good week overall!! 😁
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Today I held a pipette in my hands for the first time since undergrad, am I... a real virologist?? 🤯😱
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Great to see this published in
@NatureComms
! During my short time at
@SystemsVirology
I helped with some SC2 variants work. Although variants will keep coming, BQ.1.1 let us look into a very interesting evolutionary process of the virus, convergence!
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I'm not too bothered about these myself, but I think it's important to highlight how much abuse and personal attacks scientists receive from these conspiracy theorists. These are comments under a thread of mine completely unrelated to SC2 origins whatsoever...
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wow... this is a truly horrible take from all this, given that the hearing was an anti-science attack solely motivated by US politics. the politicians spew incoherent gibberish and disinformation and just like Eisen's take what they said had nothing to do with covid origins...
nobody seems to want to simultaneously acknowledge two truths about COVID origins: 1) that senior scientists, to some tangible extent, seem to have coordinated in the spinning of a story for a high profile publication and 2) this is a normal, everyday practice in modern science
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First things first, I was never consulted about this report or had any knowledge of it before the last 24 hours.
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Just boarding a flight to my very first in person international 🌎 conference and I'm really excited to finally see a lot of people I've worked with throughout the pandemic in the flesh for the first time! ✈️✈️
#UCSDdynamics
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Woo! 🎉🎉getting this published has been a journey (let alone during a pandemic...), but it's now out in
@PLOSBiology
!! Huge pleasure working with some great people
@OscarMacLean1
@sergeilkp
@LemeyLab
@maciekboni
@robertson_lab
I'll be posting a summary 🧵v soon!
Nice to see this out of preprint limbo: Natural selection in the evolution of
#SARSCoV2
in bats created a generalist virus and highly capable human pathogen
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2. The report states how 'the earliest variants of SARS-CoV-2 were well-adapted for human-to-human transmission' and how this 'represent a significant break from the precedent of other zoonotic spillovers involving respiratory viruses', but this is largely misleading...
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this is only one of many examples where changes that increase infectivity in a host take place before the host switch (if 'human-adapted' changes had to be engineered in a lab we wouldn't have any zoonotic pandemics anyway...)
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So, the report is being rather disingenuous about how different the COVID-19 pandemic is to other historical large-scale pandemics.
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On our way to Valencia for
@EVirusBioinfC
#ViBioM2023
✈️✈️
@Kieran12Lamb
Unfortunately we'll be a bit too late for the welcome reception tonight, but hope to see everyone tomorrow morning for some exciting Virus Bioinformatics talks and posters!! 😁😁
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Interested in our work on SARS-CoV-2 origins and ancestral recombination, but don't have time to read the preprint? You can have a listen to my talk at
#humanviruses
dynamics and evolution from a few weeks ago instead! 😁
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These 'human-adapted' changes however most likely happened in the respective animal hosts BEFORE the viruses spilled over into humans (with the earliest known 1918 pandemic sequences having the human-adapted residue: )
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If you were looking for a comprehensive review of SARS-CoV-2's origins, emergence and evolution look no further! An easy to follow piece of work by Eddie Holmes that covers what we know so far.
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Looking preppy next to my very first in person poster!
@EMBO
's first codon usage workshop has been a fantastic meeting where I got to meet a lot of new people and hear about some very exciting science!
#EMBO_CU22
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what we find is that the recombination-free closest common ancestor (recCA) to each virus is basically of equal identity ~99%, while the whole-genome similarity between SC2 and its closest bat virus (~97%) is higher than that of SC1 and its closest bat virus (~96%)
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This paper is such a good example of capturing the effect of socioeconomic changes to ecological disruption that can lead to potential zoonosis.
And also a thinking about the ongoing H5N1 spread in cattle
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After a couple of fun days in Tokyo the
@CVRinfo
team has made it to Karuizawa for the
#awaji2023
meeting! Excited to discuss the latest research on virology and Immunology!
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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.
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During my last few months in Glasgow
@angie_rasmussen
came to visit and we had a chance to do a podcast together 🎙️🎙️! Some very insightful discussion about viruses, careers, moving places and more!
Worth a listen especially for the aspiring virologists! 😁
🎙️ NEW | CVR meets
@angie_rasmussen
!
In this
@CVRGoesViral
podcast, Angie speaks about dealing with toxic bosses, sustained research investments, empowering underrepresented groups & connecting with colleagues across disciplines through social media.
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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
🦠🧬
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Had an amazing time presenting in person at
#SocialViruses
! thanks
@AsherLeeks
and
@sociovirology
for organising such a fantastic conference! Was an excellent opportunity to meet some awesome scientists that I hope to meet again in the near future!
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Had the opportunity to present some exciting new work on the importance of recombination for understanding CoV origins and how to integrate sampling information to our approaches while at the 7th
@WOHCongress
in Singapore last week!
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🔔🔔🔔NEW PREPRINT ALERT! From the vault, a wee study
@SejModha
and I have been working on in the background for a while now: Diversity and evolution of the human anellome
@biorxivpreprint
The story goes...
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Short stop at a very familiar place!! 🏴🏴
Quite funny to be giving an external seminar at the
@CVRinfo
just 6 months after I left! 😂
Great to see lots of colleagues and friends and discuss some exciting science!!
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One paper (me) and two grant proposals (
@KawakuboShusuke
) submitted!! Worth a Monday celebration! 🎉🎉
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Talk day for the
@CVRinfo
representatives!
#ECV2023
catch
@annasimsbiol
speaking about superinfection exclusion at 2:45 in Sala Koncertowa and me speaking about ancient bat genes at 4:50 in Sala Biala!
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Check out our latest paper! A deep dive into the recombinant origins of MERS-CoV's Spike protein 🐫🦠 and overall patterns of recombination across the 🦇MERS relatives! Congratulations Jarel for leading this work!! 🎉🎉
NEW PUBLICATION ‼️ 🦠
We are delighted to share our findings on the influence of recombination on the receptor switching event of MERS-CoV and its close relatives. This paper is now out in
@VirologyJ
.
Please see the threads ⬇️ for some explanation (1/11)
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AI, 33,000 protein structures and a hypothesis for how Flaviviridae glycoproteins evolved over their 1Byr history!
Happy to have contributed to this fantastic preprint led by
@jonathon_mifsud
and
@GroveLab
during my brief time at the Grove Lab
@CVRinfo
!
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We recently performed a very comprehensive analysis to see, once you account for the complex recombination patterns in these viruses, how close sampled animal sarbecoviruses are to SC1 and SC2 respectively:
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As an author on the preprint this is both hilarious and f'ing mad! Spotted it weeks ago and ofc knew it wasnt Eddie, cause whoever wrote this has absolutely no clue what they're talking about...
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Wow! 🎉🎉I sure wasn't expecting this!! But I'm very grateful for this award and I'd like to thank the
@EVirusBioinfC
organising committee for putting together this excellent conference!! We'll hopefully see each other in person next year!
We are very happy to close
#ViBioM2022
by announcing the Best ECR Talk Award which goes to
@SpyrosLytras
and three Best Poster Awards that go to
@nishimura_luca
,
@CliaPas1
, and
@gabriellovate
🎉👏🥳🍾
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this is a different story to SARS-CoV-2's essentially one-off spillover. The genetic data support that SC2 was introduced in humans in 2 spillover events, BUT these 2 events happened at almost the same time from a single host population source:
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Look what came in the mail this morning! Thank you again
@EVirusBioinfC
for an excellent conference and for giving me this award! Really nice gesture to have this in physical form and 🤞🤞 for an in person conference next year!
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So good to be back in Tokyo for a quick visit, seeing friends and chatting exciting science!! Thanks
@SystemsVirology
for hosting us and for the great food! 😁
A lunch party in my lab🇯🇵🇬🇧🏴🇩🇪🇫🇷🇵🇭🇹🇭🇨🇳🇮🇩🇺🇸
Welcome guys
@SpyrosLytras
@robertson_lab
@NchiouaRayhane
🙂!!!
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We put together a
@virological_org
post (in two parts) about the mutations of
#omicron
and what they might mean, led by
@DarrenM98230782
&
@sergeilkp
+ many expert co-authors (the most people I've ever seen editing a single google doc at the same time)
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After almost 4 years at the
@CVRinfo
I haven't had a chance to attend one of the infamous
#GlasgowVirologyWorkshop
until today! 😁 Looking forward to some very exciting virus talks!
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Since everyone in the UK seems to be posting these, here's mine.... 😩😩 I guess no
#Microbio22
for me... But at least I'm feeling ok!
#VaccinesWork
Now just need to make sure I don't drive myself crazy during isolation! 🤞😅
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Come chat about bat sarbecovirus movement, recombination and phylogenetics at tonight's poster session! P51!
📢
#Nido2023
| Some of our team are at the International Nidovirus Symposium in Switzerland!🇨🇭
Don't forget to say hello and read their fabulous posters if you're there too!
@nidovirus2023
@SpyrosLytras
@herdervanessa
@WFurnon
@NessaDun1
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thus the comparison to different H7N9 viruses spilling over from farmed birds repeatedly but months apart is irrelevant (not to mention the date typos that make you wonder if anyone proof-read this report...)
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Delighted to be an invited speaker at the
@Els_Vaccine
17th Vaccine Congress, here in Glasgow! 💉 Looking forward to discussions bridging vaccine development, one health and evolutionary virology! Catch my talk on Wednesday morning! 😁
#17vaccinecongress
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Clear, but complex, evidence has been consistently accumulating for one side in the past 3.5 years. What's even clearer is the complete lack of evidence for the other side!
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So great to see this exciting preprint that I've heard a lot about (probs cause I spend too much time chatting to
@Kieran12Lamb
...) finally up on
@biorxivpreprint
!
SARS-CoV-2's evolutionary capacity is mostly driven by host antiviral molecules ✏🧬
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Happy holidays 🎄 with a new cool preprint from my time at the
@SystemsVirology
lab! In this piece we describe the characteristics of SC2 variant XBB that's widely circulating rn
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CoVs seem to recombine so much in nature that looking for a 'full genome closest relative' to SARS-CoV-2 is futile. However, we can split genomes into the best 'non-recombinant' segments and estimate evolutionary relatedness to animal viruses for each one of them:
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Following our
@virological_org
post from a week back or so, we have now released the preprint version with extended text + supplementary
a short 🧵1/9
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4. My final point is about how similar our understanding of the SARS-CoV-1 emergence origins is compared to that of SC2, since the report makes it sound like we know everything about SC1 and nothing about SC2 origins...
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Enjoying my overpriced airport Asahi before setting off for my first conference tour representing the
@SystemsVirology
lab!!
First stop Leuven for
@EVirusBioinfC
#ViBioM2024
looking forward to seeing many friends and collaborators! 😁
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Delighted to be giving the first
@VirologyWakate
journal club! I'll be talking about a cool evolutionary arms race story between SARS-CoVs and bat immune systems I worked on with
@WilsonLabCITIID
during our time at the
@CVRinfo
!
This Wed, 7pm Japan time, register below ⬇⬇⬇
We are inviting everyone, especially the young virologists worldwide, to join us for the very first journal club of Wakate Young Virologists Network. Our first speaker is Dr. Spyros Lytras
@SpyrosLytras
of
@SystemsVirology
Lab. Please repost! 🦠
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3. There is a rather odd comparison between the COVID-19 pandemic and the H7N9 flu epidemics in China
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Very grateful to be representing our centre
@CVRinfo
at the
#QAPrizes2022
ceremony! ✨✨
We’re honoured to be a
#QAPrizes2022
winner!🏆
Last night some of our amazing team attended the
@qaprizes
dinner to celebrate this achievement alongside fantastic teams from universities & colleges across the UK.
Find out more about our prize here:
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alrighty the seqs are on NCBI and I've had a look! BANAL103 is THE closest for that frag3, having 39bp diffs on a 1281bp fragment. Using the rate we have previously estimated for the nCoV clade this gives a (very rough) estimate of ~12 years of divergence! (getting closer!!)
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).
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cattle
#h5n1
update!! very impressive analysis by the
@USDA_APHIS
team in such short time!
single introduction ~4 months ago, cattle to mammal spills, spread through cattle movement.
Wish the SI was available... can't find them on
@biorxivpreprint
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Glasgow visit was short but sweet! Lovely to see lots of people and hear some fantastic talks at
#glasgowvirologyworkshop
including
@lucygthorne
@ArisKatzourakis
@VHIT_Mckimmie
! Although the best part was the ceilidh!! 🕺💃
Now off to my final (and warmest destination 👀👀)
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Thanks for the very warm welcome! Great to be visiting the
@SystemsVirology
lab in Tokyo 🇯🇵 for a few weeks to do some exciting science! (and eat some delicious food 😁)
Fun time with all lab members🇯🇵 as well as a new student from China🇨🇳 and two visitors from Scotland🏴 (originally from Greece🇬🇷) and Germany🇩🇪. How becoming international it is🌏! Enjoyed homemade meals from their countries as well🍽. Welcome guys to my lab!! Let us have fun👍
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My first year in the official
@SystemsVirology
lab photo!! (can you spot me?) 📸📸
Here is the Sato Lab, 2024!😎
🇦🇺🇨🇳🇯🇵🇨🇳🇯🇵🇯🇵🇵🇭🇯🇵🇯🇵🇯🇵🇯🇵🇯🇵🇯🇵🇨🇳🇬🇷🇯🇵🇯🇵🇯🇵🇯🇵🇯🇵🇯🇵🇨🇳🇹🇭🇯🇵🇺🇸🇯🇵🇯🇵🇹🇭🇵🇭🇯🇵🇯🇵🇯🇵🇮🇩
The sunny sky☀️ was created by AI😆
(thanks Spyros
@SpyrosLytras
for that ☀️)
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What a fantastic time
#ViBioM2024
has been! Excellent organisation, fantastic talks and great people to chat with about lots of exciting science!
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Before heading to Cambridge I had a nice chance to visit St Mary's Hospital
@imperialcollege
, where Fleming discovered penicillin(!!!), and chat about cool coronavirus science over coffee with
@lucygthorne
! Thanks for having me! 😁🦠☕
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Before we get started, for a non-technical explanation of the results here's a wee video of me handwaving about recombination
📖 NEW PUBLICATION | Natural origins of SARS-CoV-2 in
@GenomeBiolEvol
@SpyrosLytras
,
@robertson_lab
& colleagues disentangle the complex evolutionary history of
#SARSCoV2
&
#coronaviruses
🦠
Watch Spyros explain the research👇
#CVRCovidResponse
Read:
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