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

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.”

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@pathoplexus.org · 2w ago

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

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...

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

Here is a difficult one… guess the city

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!

Trinket@trinketbirdy.bsky.social · 2mo ago

No seriously they're stuck in a shit pub being yelled at by Fatboy Slim

The average wealth of a Fellow of the @royalsociety.org is now over 0.5 billion dollars.

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

arguably.uk

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/

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

science.org

The ARTIC Primer Foundry is now live and will soon begin shipping BDBV primers on request primalscheme.com/orders

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

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

🎧 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

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...

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 ...

virological.org

A timely review of Matt Ridley's arguments and book. An engaging read.... www.the-gallop.com/review-matt-...

Converting images to trees has a long history. @arambaut.bsky.social wrote TreeThief many years ago, @bljog.bsky.social released TreeRipper over a decade ago doi.org/10.1186/1471..., the list goes on. All because people don't share machine readable phylogenies 😞

TreeRipper web application: towards a fully automated optical tree recognition software - BMC Bioinformatics

Background Relationships between species, genes and genomes have been printed as trees for over a century. Whilst this may have been the best format for exchanging and sharing phylogenetic hypotheses during the 20th century, the worldwide web now provides faster and automated ways of transferring and sharing phylogenetic knowledge. However, novel software is needed to defrost these published phylogenies for the 21st century. Results TreeRipper is a simple website for the fully-automated recognition of multifurcating phylogenetic trees ( http://linnaeus.zoology.gla.ac.uk/~jhughes/treeripper/ ). The program accepts a range of input image formats (PNG, JPG/JPEG or GIF). The underlying command line c++ program follows a number of cleaning steps to detect lines, remove node labels, patch-up broken lines and corners and detect line edges. The edge contour is then determined to detect the branch length, tip label positions and the topology of the tree. Optical Character Recognition (OCR) is used to convert the tip labels into text with the freely available tesseract-ocr software. 32% of images meeting the prerequisites for TreeRipper were successfully recognised, the largest tree had 115 leaves. Conclusions Despite the diversity of ways phylogenies have been illustrated making the design of a fully automated tree recognition software difficult, TreeRipper is a step towards automating the digitization of past phylogenies. We also provide a dataset of 100 tree images and associated tree files for training and/or benchmarking future software. TreeRipper is an open source project licensed under the GNU General Public Licence v3.

doi.org

The Proximal Origin of the MV Hondius Andes virus outbreak. virological.org/t/potential-...

Potential geographical and ecological origin of the MV Hondius Andes virus outbreak

The recent outbreak aboard the MV Hondius caused by Andes virus raises two key questions [1]: (i) where do the outbreak genomes cluster geographically, and (ii) how can the phylogenetic signal be reco...

virological.org

Initial genomic characterization of the Bundibugyo virus outbreak in Eastern DRC with cases in Uganda. Join work between INRB in DRC and CPHL in Uganda plus many partners. virological.org/t/initial-ge...

Rapid release of multiplex PCR amplicon scheme for Andes hantavirus whole genome sequencing validated on control material: www.biorxiv.org/content/10.6... @scalene.bsky.social @stevepullan.bsky.social @ukhsa.bsky.social output from HPRU in Public Health Genomics

1/ 🚀 Pathoplexus now supports the Andes variant of Hantavirus (ANDV). ANDV is the variant identified in the recent MV Hondius cases, & the Hantavirus variant previously identified as having occasional human-to-human transmission. pathoplexus.org/andv #hantavirus #hondius

First genome sequence from Andes hantavirus strain from ongoing ship outbreak posted on Virological: virological.org/t/complete-s... courtesy Swiss National Reference Centre for Emerging Viral Infections, Geneva University Hospitals, University of Zurich

Complete sequence of Orthohantavirus andesense virus: Swiss resident 2026

Posted on behalf of the Swiss National Reference Center for Emerging Viral Infections, Geneva University Hospitals and the Institute of Medical Virology, University of Zurich (Partner Laboratory Natio...

virological.org

Complete genome of the Hondius outbreak hantavirus (and tree): virological.org/t/complete-s...

Complete sequence of Orthohantavirus andesense virus: Swiss resident 2026

Posted on behalf of the Swiss National Reference Center for Emerging Viral Infections, Geneva University Hospitals and the Institute of Medical Virology, University of Zurich (Partner Laboratory Natio...

virological.org

IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...

IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models

Abstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih

academic.oup.com

In March, invited by Jay Bhattacharya, Matt Ridley gave the inaugural "Scientific Freedom Lecture" at NIH, on a lab leak origin of COVID-19. There was a lot to debunk; here is Part II: pandemonium.hypotheses.org/1108 🧪 #covidorigin

Fact-checking Matt Ridley’s “Scientific Freedom Lecture” at NIH (Part II)

The first part of this rebuttal can be read here; the third part will be posted later. Ridley’s lecture is available on Youtube; I also generated a transcript, available here. The same disclaimer as i...

pandemonium.hypotheses.org

I have been really impressed with @beaconbio.bsky.social, and find myself using it more and more. Excellent resource to replace ProMED.

There was literally a pangolin that flew combat sorties with the CIA in a dirty war in Laos that then died after drinking too much gin, so there’s at least one pangolin whose record is morally ambiguous

Jenny Hamilton@readingtheend.bsky.social · 4mo ago

fun fact: no pangolin has ever done a single thing wrong in the entire history of the world

@ucuedinburgh.bsky.social @ucu.org.uk Sounds familiar?

Simon J. Greenhill@simongreenhill.bsky.social · 4mo ago

Do you know a university cutting roles because 'urgent financial crises'? Don't believe them: ANU made up their crisis & forced massive cuts for NO reason & with NO plan. So many friends and colleagues suffered (& still do) because of this malice. Criminal. www.abc.net.au/news/2026-03...

Do you know a university cutting roles because 'urgent financial crises'? Don't believe them: ANU made up their crisis & forced massive cuts for NO reason & with NO plan. So many friends and colleagues suffered (& still do) because of this malice. Criminal. www.abc.net.au/news/2026-03...

Draft report into ANU's controversial cuts critical of university's council

ANU's council approved a massive $250 million cost-cutting program without clear evidence it was needed or achievable, according to an assessment in a draft audit office report.

abc.net.au