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arambaut.bsky.social
Andrew Rambaut (🐏🎀)
@arambaut.bsky.social
2.8K followers 380 following 290 posts
Virus evolution | genomic epidemiology| virus origins | phylogenetics | BEAST | ARTIC Network

University of Edinburgh

http://beast.community
http://artic.network
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Reposted by Andrew Rambaut (🐏🎀)
kgandersen.bsky.social
This is the worst news I have heard in a very long time - what a tragic loss.

@helenbranswell.bsky.social was, unquestionably, _the_ best in the field and just a wonderful person.

Condolences to her family and colleagues - she'll be sorely missed.

www.statnews.com/2026/10/13/h...
Helen Branswell, whose reporting on infectious diseases and public health drew acclaim, dies at 69
Helen Branswell, STAT's infectious disease reporter who earned the respect of experts and public health officials with her accessible, prescient dispatches, has died at age 69.
www.statnews.com
October 13, 2026 at 6:33 PM
arambaut.bsky.social
Following up from my thread about a new version of my phylogenetic tree viewer, PearTree, that was developed using extensive use of LLMs...

bsky.app/profile/aram...
arambaut.bsky.social Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 14d
For transparency - this was coded from scratch with extensive use of various LLMs but in a framework with which I am very familiar (browser-based Javascript). So I was able to assert design patterns, code re-use and modularity which I am happy with and feel I can modify manually if needed.
October 13, 2026 at 3:48 PM
arambaut.bsky.social
Version 1.3.2 of PearTree released: github.com/artic-networ...

Fixes many of the remaining niggling bugs. WebApp updated at peartree.live
The logo of the PearTree phylogenetic tree viewer app - a partridge in a pear tree.
October 13, 2026 at 3:28 PM
arambaut.bsky.social
"Temporal and Phylodynamic analyses of the 2026 Bundibugyo virus disease outbreak in the
Democratic Republic of the Congo" - www.medrxiv.org/content/10.6...
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...
www.medrxiv.org
October 9, 2026 at 3:38 PM
arambaut.bsky.social
The previous ebolavirus outbreak in DRC - only a year ago:
lancetmicrobe.bsky.social The Lancet Microbe @lancetmicrobe.bsky.social · 27d
New research article

Epidemiology and phylogenomic characterisation of the 2025 #Ebola virus disease outbreak in Bulape, Kasaï province, Democratic Republic of the Congo: a retrospective observational study

www.thelancet.com/journals/lan...

#IDSky #ClinMicro #MicroSky #ViroSky #OpenAccess #OA
September 30, 2026 at 11:44 AM
Reposted by Andrew Rambaut (🐏🎀)
natmicrobiol.nature.com
Out Now! A generalized lineage nomenclature for viral genomic epidemiology #MicroSky
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.
go.nature.com
September 30, 2026 at 10:04 AM
Reposted by Andrew Rambaut (🐏🎀)
clauswilke.com
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...
It still wasn’t a lab leak
Six years in, all the evidence points in one direction
blog.genesmindsmachines.com
September 15, 2026 at 1:59 PM
Reposted by Andrew Rambaut (🐏🎀)
tetherin.bsky.social
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...
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.
www.bloomberg.com
September 1, 2026 at 12:44 PM
Reposted by Andrew Rambaut (🐏🎀)
clauswilke.com
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...
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
blog.genesmindsmachines.com
August 30, 2026 at 3:42 PM
Reposted by Andrew Rambaut (🐏🎀)
snpoehlm.bsky.social
🧪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.🧵
August 25, 2026 at 1:39 PM
Reposted by Andrew Rambaut (🐏🎀)
kgandersen.bsky.social
Everything you might ever want to know about the furin cleavage site in SARS-CoV-2.
snpoehlm.bsky.social Stefan Pöhlmann @snpoehlm.bsky.social · Aug 25
🧪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.🧵
August 25, 2026 at 2:24 PM
arambaut.bsky.social
And a close up (diamond ring stage)...
August 12, 2026 at 8:12 PM
arambaut.bsky.social
Segovia cathedral, an eclipse, and Venus…
The solar eclipse over Segovia, Spain
August 12, 2026 at 7:31 PM
Reposted by Andrew Rambaut (🐏🎀)
flodebarre.eurosky.social
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
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...
pandemonium.hypotheses.org
August 4, 2026 at 8:17 PM
Reposted by Andrew Rambaut (🐏🎀)
michaelhobbes.bsky.social
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.”
July 30, 2026 at 1:33 PM
arambaut.bsky.social
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.
pathoplexus.org Pathoplexus @pathoplexus.org · Jul 23
2/ 📄 SeqSets/DOIs now show citations! We've integrated with @crossref.bsky.social so you can see which scientific publications have used a SeqSet - on the SeqSet page *and* on individual sequence pages.

Using seqs in a paper? Don't forget to cite the DOI! 👉 pathoplexus.org/about/citation
Screenshot of a SeqSet page, showing that the SeqSet has been cited in a paper, with a link to that paper. Screenshot showing the 'cited in' section on a sequence page - showing the paper a sequence was used in, and a link to that paper.
July 23, 2026 at 10:22 AM
Reposted by Andrew Rambaut (🐏🎀)
onisillos.bsky.social
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…
July 14, 2026 at 9:23 AM
Reposted by Andrew Rambaut (🐏🎀)
artic.network
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...
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...
virological.org
July 9, 2026 at 3:04 PM
arambaut.bsky.social
Here is a difficult one… guess the city
A picture of an a city with one or two identifiable landmarks.
July 5, 2026 at 5:56 PM
Reposted by Andrew Rambaut (🐏🎀)
isabelott.bsky.social
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!
trinketbirdy.bsky.social Trinket @trinketbirdy.bsky.social · Jun 13
No seriously they're stuck in a shit pub being yelled at by Fatboy Slim
June 13, 2026 at 8:23 PM
arambaut.bsky.social
The average wealth of a Fellow of the @royalsociety.org is now over 0.5 billion dollars.
June 12, 2026 at 11:49 AM
Reposted by Andrew Rambaut (🐏🎀)
gsoh31.bsky.social
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-...
The quiet collapse of British universities
One of our great triumphs and economic advantages is fading away
www.arguably.uk
June 11, 2026 at 9:08 AM
Reposted by Andrew Rambaut (🐏🎀)
royalsociety.org
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 https://royalsociety.org/people/joseph-felsenstein-38106/
June 5, 2026 at 7:03 AM
Reposted by Andrew Rambaut (🐏🎀)
kgandersen.bsky.social
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...
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
www.science.org
June 4, 2026 at 7:07 PM
Reposted by Andrew Rambaut (🐏🎀)
artic.network
The ARTIC Primer Foundry is now live and will soon begin shipping BDBV primers on request primalscheme.com/orders
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.
primalscheme.com
June 1, 2026 at 10:21 AM