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Andrew Rambaut (🐏🎀)

@arambaut.bsky.social
2.8K followers 380 following 266 posts

Virus evolution | genomic epidemiology| virus origins | phylogenetics | BEAST | ARTIC Network University of Edinburgh beast.community artic.network

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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 10/10/2026
Some hints through the clouds above Rum.
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 09/10/2026
For the latest phylogenetic/phylodynamic analysis (as well as a large range of other epidemiological data visualisations) see the INRB Epidemic Intelligence Dashboard - inrb-umie.github.io/BDBV2026-Epi...
inrb-umie.github.io
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 09/10/2026
"Temporal and Phylodynamic analyses of the 2026 Bundibugyo virus disease outbreak in the Democratic Republic of the Congo" - www.medrxiv.org/content/10.6...
medrxiv.org
Temporal and Phylodynamic analyses of the 2026 Bundibugyo virus disease outbreak in the Democratic Republic of the Congo
The Democratic Republic of the Congo is experiencing a major outbreak of Ebola disease caused by Orthoebolavirus bundibugyoense (Bundibugyo virus), which was declared on May 15, 2026. To investigate t...
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 30/09/2026
The previous ebolavirus outbreak in DRC - only a year ago:
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Nature Microbiology @natmicrobiol.nature.com · 30/09/2026
Out Now! A generalized lineage nomenclature for viral genomic epidemiology #MicroSky
go.nature.com
A generalized lineage nomenclature for viral genomic epidemiology
Nature Microbiology, Published online: 30 September 2026; doi:10.1038/s41564-026-02468-3This study extends the Pango lineage nomenclature system beyond SARS-CoV-2, introducing a dynamic framework for tracking and communicating viral diversity, demonstrated through its application to CHIKV.
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 16/09/2026
I love the innovative use of the annoying extra 'a' for 'and' in the acronym.
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Claus Wilke @clauswilke.com · 15/09/2026
I wrote up my thoughts about the COVID origin. I don't plan to weigh in on the topic beyond this one post for the next five years or so. Looking into what the evidence says once or twice every decade feels like a good cadence. blog.genesmindsmachines.com/p/it-still-w...
blog.genesmindsmachines.com
It still wasn’t a lab leak
Six years in, all the evidence points in one direction
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 02/09/2026
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Stuart Neil @tetherin.bsky.social · 01/09/2026
Fantastic article about the life and work of Bob Garry that highlights both the personal and scientific costs that the conspiracy theory industry has had on Global public health and the scientists who have dedicated their lives to fighting infectious diseases www.bloomberg.com/news/feature...
bloomberg.com
A Top Virus Scientist Stared Down Covid Lab-Leak Proponents. Now His Life’s Work Is at Stake
The battle over Covid’s origins has come for Bob Garry, who’s faced some of the world’s deadliest viral threats.
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Claus Wilke @clauswilke.com · 30/08/2026
I'm really frustrated by the constant fear-mongering about AI-designed superviruses. Can we focus on the things that should actually worry us, such as measles? blog.genesmindsmachines.com/p/im-sorry-y...
blog.genesmindsmachines.com
I'm sorry, you're not going to die from an AI-engineered supervirus
God save us from economists who think they can competently talk about biology
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Stefan Pöhlmann @snpoehlm.bsky.social · 25/08/2026
🧪An exciting new preprint offers insights into how SARS-CoV-2 and other coronaviruses can acquire cleavage motifs for the cellular protease furin. A thread on the importance of the furin motif in the SARS-CoV-2 spike and its possible origins.🧵
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Kristian G. Andersen @kgandersen.bsky.social · 25/08/2026
Everything you might ever want to know about the furin cleavage site in SARS-CoV-2.
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 25/08/2026
They definitely exist: Relman: "the fact that publications by Chinese researchers indicate knowledge about the Sars-CoV-2 virus before late December 2019" www.theguardian.com/commentisfre... ...but they don't seem to be on GoogleScholar.
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 13/08/2026
I wonder if a whale fin identification machine learning classifier would work on these people's weird (but possibly unique) pattern of bits and bobs on their chests? www.nature.com/articles/s41...
nature.com
FIN-PRINT a fully-automated multi-stage deep-learning-based framework for the individual recognition of killer whales - Scientific Reports
Scientific Reports - FIN-PRINT a fully-automated multi-stage deep-learning-based framework for the individual recognition of killer whales
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 12/08/2026
And a close up (diamond ring stage)...
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 12/08/2026
Segovia cathedral, an eclipse, and Venus…
The solar eclipse over Segovia, Spain
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Flo Débarre @flodebarre.eurosky.social · 04/08/2026
Today is the first Tuesday of the month, my (self-imposed) blog posting day -- I wrote about accusations of coverup and conspiracies, thrown without any evidence, in the context of the recent release of private documents by Rand Paul #covidorigin
pandemonium.hypotheses.org
Conspiracies and coverups
There is no evidence for a lab origin of SARS-CoV-2, so commenters default to meta-discourse and accuse scientists of coverups, for which there is no evidence either. So far, available data and scient...
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 04/08/2026
Exactly? Fixed it for you...
The image with DNA molecules reflected.
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Michael Hobbes @michaelhobbes.bsky.social · 30/07/2026
The scientists then published a research paper demonstrating that the virus showed no signs of being engineered. This paper has not been debunked or retracted. No evidence of engineering has emerged. In the conclusion the paper says, “but it could still be a lab leak.”
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 23/07/2026
This is so important - allowing individual uses of data to be tracked as citations will be so useful for demonstrating impact and reach of genome data. When you use data from Pathoplexus, create a SetSet & DOI for the sequences used and cite it in your paper.
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 18/07/2026
Do all mathematicians get trained to write equations in mirror writing on glass walls?
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Onisillos @onisillos.bsky.social · 14/07/2026
As I was foolish enough to read the recent Atlantic article on covid origins, I will re-share my takes on this topic to cleanse myself: www.thelancet.com/journals/lan... and www.thelancet.com/journals/lan...
SARS-CoV-2 is a natural virus that found its way into humans through mundane contact with infected wildlife that went on to cause the most consequential pandemic for over a century. While it is scholarly to entertain alternative hypotheses, particularly when evidence is scarce, these alternative hypotheses have been implausible for a long time and have only become more-so with increasing scrutiny. Those who eagerly peddle suggestions of laboratory involvement have consistently failed to present credible arguments to support their positions.
Take the time to reflect on the paragraph above and how many words were expended to make the simple point that COVID-19 had a natural origin. This is because there are many people, most notably in the USA, with disproportionate influence who are poised to seize on less explicit statements to undermine a simple, and pretty straightforward, truth. These are the same people who are willing to malign individuals—a topical example being former director of the National Institute of Allergy and Infectious Diseases Anthony Fauci—who dedicated themselves to understanding and lessening the impact of the pandemic.
The sheer hubris needed to underpin alternative hypotheses was an early signal of their tenuousness, when we are intensely aware that the natural processes needed to bring about this sort of pandemic are constantly churning and testing the boundaries between animal and human populations. The most remarkable thing about the whole COVID-19 origin saga is the confected controversy over something that should not be controversial at all. The thing that should be controversial is how little of the energy expended over this discussion has been directed towards actual beneficial outcomes.
To be frank, the fanciful ideas put forward by self-described free thinkers are more in keeping with popular movies than the realities of working with pathogens. It is admirable to pursue curiosity wherever it might lead and to reject the constraints of…A year ago, August 2024, we addressed the state of discussions about COVID-19 origins in our Editorial COVID-19 origins: plain speaking is overdue. We did not lay out the evidence because the space we had available was not sufficient to address the points in detail. And the evidence was presented in a comprehensive and digestible fashion by the authors of the relevant research. Our focus was laying out the situation in a clear and uncluttered way, to counter the many commentators in the press who were giving their assessments based on what they wanted to believe (or what would make a more entertaining story) rather than what they could back up with evidence. Given the potential consequences, to pandemic prevention and public health in general, they were being irresponsible.
On June 27, 2025, WHO’s Scientific Advisory Group for the Origins of Novel Pathogens (SAGO) published their report Independent Assessment of the Origins of SARS-CoV-2. This report provides an update in the context of information that has emerged since their 2022 report. The report outlines the most prominent hypotheses and reflects on the supporting evidence for each of them. They stress that they did not have access to raw data when preparing this report, and SAGO and WHO have requested further information from governments, including those that have made assertions about the origins of SARS-CoV-2: China, Germany, and the USA. At the time of writing the report this information had not been provided. Meaning that this report is based on published literature, not so-called intelligence touted by some governments.
The report outlines four hypotheses but essentially two are based on zoonotic spillover and two are based on a laboratory accident. The assessment in the report from the outset discounts one hypothesis from each of these broad categories due to a lack of evidence, although SAGO remains open to reconsideration if more evidence is forthcoming. Despite giving one of the laboratory accident…
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ARTIC network @artic.network · 09/07/2026
139 genomes now sequenced from the ongoing 2026 Bundibugyo virus disease outbreak in DRC, spanning 16 Health Zones. Led by INRB with support from the ARTIC network (Wellcome Trust and Gates Foundation). Full analysis: virological.org/t/genomic-ep...
virological.org
Genomic epidemiology of the ongoing 2026 Bundibugyo Virus Disease outbreak in the Democratic Republic of the Congo
Genomic epidemiology of the ongoing 2026 Bundibugyo Virus Disease outbreak in the Democratic Republic of the Congo Institut National de Recherche Biomédicale (INRB), Kinshasa – DRC and partners Conte...
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 05/07/2026
Is there football on?
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 05/07/2026
Here is a difficult one… guess the city
A picture of an a city with one or two identifiable landmarks.
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 05/07/2026
I recommend one of ones that overlook the Botanical Gardens at the back. I am sure they are affordable.
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 27/06/2026
Thanks! You might like to try PearTree - peartree.live or desktop versions at github.com/artic-networ...
peartree.live
PearTree — Phylogenetic Tree Viewer
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 18/06/2026
One of these?
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 17/06/2026
And you should pick up some tablet from Edinburgh for your return. Fudge House on Royal Mile or Candersons on Leith Walk - both good sources.
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Isabel, booonyavirus wonk @isabelott.bsky.social · 13/06/2026
Unsurprising to anyone acquainted with the start of Fatboy Slim’s musical career: playing bass in The Housemartins, an openly socialist indie rock band. As their best-known hit – an a capella cover of an R&B song – declared: everybody take a stand, & join the caravan of love!
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 13/06/2026
Counting down for a Glaswegian to say "Glasgow"...
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 13/06/2026
www.realmarykingsclose.com
realmarykingsclose.com
The Real Mary King's Close | Best UK Attraction
Welcome to The Real Mary King's Close. One of Edinburgh's top attractions and only preserved 17th-century street.
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 13/06/2026
Mary's Milk Bar on Grassmarket (below the Castle) for the best gelato.
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 13/06/2026
If it is wet (I am sure it won't be) then the National Museum and the Museum of Scotland (next to each other) are great - the latter in particular. See Dolly the Sheep.
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 13/06/2026
Walk across Holyrood Park (Salisbury Craigs and Arthur's Seat - the old volcano for some geology - www.scottishgeologytrust.org/geology/51-b...) and then to Duddingston for lunch/skittles at the Sheep Head Inn.
scottishgeologytrust.org
Holyrood Park, Edinburgh – Scottish Geology Trust
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 13/06/2026
If you go to North Berwick you can do the boat out to the Isle of May for sea birds.
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 13/06/2026
Art and museums - www.jupiterartland.org in particular for kids.
jupiterartland.org
Edinburgh's Award-Winning Contemporary Sculpture Garden
Experience Edinburgh's award-winning sculpture garden. Explore contemporary art across 120 acres of meadow, woodlands and indoor galleries.
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 12/06/2026
The average wealth of a Fellow of the @royalsociety.org is now over 0.5 billion dollars.
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Glen O'Hara @gsoh31.bsky.social · 11/06/2026
Today I've written for Arguably on one big mystery in our public life: why does no-one care about the existential crisis of our universities? Read all about it... 👇 www.arguably.uk/p/the-quiet-...
arguably.uk
The quiet collapse of British universities
One of our great triumphs and economic advantages is fading away
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The Royal Society @royalsociety.org · 05/06/2026
Professor Joe Felsenstein FRS is elected a Fellow of the Royal Society. After initially working on population genetics theory of recombination, of migration, and of speciation, his main focus has been on phylogenetic inference. #RSFellows royalsociety.org/people/joseph-fels…
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Kristian G. Andersen @kgandersen.bsky.social · 04/06/2026
This is extremely chilling - virologists being targeted for what appears to be minor (if any) "offenses". We all know _why_ this is happening, so I'm not going to belabor that point - but I want to provide some context on the technical details. 🧵 www.science.org/content/arti...
science.org
NIH scientists plead not guilty to smuggling monkeypox viruses into U.S.
Defendants face prison time for criminal charges but samples may all have been inactivated and used for routine diagnostics
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 04/06/2026
A restricted case but one of the few where sufficient training material may actually be available with explicit licensing. And a large fraction of such code is in one location - GitHub (which runs its own LLM agents which don't do this).
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 04/06/2026
A very restricted case but I could imagine a coding agent with a model that has only been trained on open-source code, following the terms of the licenses (i.e., attribution, non-commercial etc. but no Gnu licenses due to the like-for-like licensing requirement).
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ARTIC network @artic.network · 01/06/2026
The ARTIC Primer Foundry is now live and will soon begin shipping BDBV primers on request primalscheme.com/orders
primalscheme.com
PrimalScheme: primer panels for multiplex PCR
PrimalScheme is a tool for designing primer panels for multiplex PCR. It uses a greedy algorithm to find primers for tiling amplicon generation for multiple reference genomes.
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ARTIC network @artic.network · 01/06/2026
Various sequencing approaches work for BDBV: amplicon panels (BDBV-specific v1.0.0 & pan-Ebola v2.0.0), bait capture (Twist/Illumina), or metagenomics. Primer schemes are available via labs.primalscheme.com and are being synthesised for free distribution on request via the new ARTIC Primer Foundry
labs.primalscheme.com
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ARTIC network @artic.network · 01/06/2026
ARTIC network has published Bundibugyo (BDBV) sequencing resources as the 2026 outbreak continues in DRC & Uganda. We have compiled guidance for labs wishing to sequence, assemble and analyse BDBV genomes: artic.network/viruses/bdbv/bdbv-sequencing-guide.html
artic.network
Bundibugyo virus genomic sequencing resources | ARTIC network - pathogen genomics from sample to response
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Prof Gavin Yamey MD MPH @gavinyamey.bsky.social · 31/05/2026
🎧 Starting a new thread! 20 of my fave trip-hop tunes Based on its history & cultures, only one city on earth could have birthed it: Bristol Trip-hop drew on dub, soul & hip-hop & came out of sound systems—like the Wild Bunch—in mostly Black neighborhoods It spread nationally & globally 2/22
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S Otto @sarperotto.bsky.social · 31/05/2026
Globally, genomic data sharing has improved greatly over the past year for the highly pathogenic avian flu H5N1. Some great news and a major concern... virological.org/t/timely-h5n...
virological.org
Timely H5N1 sequence data now provided by many – but not all – countries
Sarah Otto* * Department of Zoology & Biodiversity Research Centre, The University of British Columbia, Vancouver BC Canada V6T 1Z4. E-mail: otto@zoology.ubc.ca A year ago, we raised concerns about ...
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 28/05/2026
Should also mention treerobber, treeburglar, treeshoplifter, treesnatcher*, treepickpocket, treemugger, treelarcenist, treestealer, treepilferer, treepoacher; treeraider, treelooter, treeplunderer, treepillager, treebandit, treepirate, and of course treehighwayman. *actually this one is real
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Jeremy Berg @jeremymberg.bsky.social · 28/05/2026
A timely review of Matt Ridley's arguments and book. An engaging read.... www.the-gallop.com/review-matt-...
the-gallop.com
Review: Matt Ridley's "Viral" Case for a Lab Leak
Matt Ridley went from calling a lab leak “slightly more probable” in 2021 to “almost certainly correct” in 2026. Yet, as his original case in Viral collapsed, his certainty now rests on a 12-nucleotide "God of the Gaps."
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