On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5

As expected, unfortunately. If ever you needed a reason for never using GISAID ever again (as a data producer or data user - we're both), look no further. Time to move on to more trusted and transparent solutions.

Our paper on the phenomenon of persistence and latency in Ebola virus in an unobserved reservoir is finally out in preprint: www.biorxiv.org/content/10.1...

And now NextStrain as well. Next up, will GISAID start charging open-source community tools to have access? That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.

If you could take just one journalist with you to a polar archipelago, who would it be? 100% @kakape.bsky.social😉 Thanks for the extensive conversations and excellent reporting. Immer wieder gerne!

Seems to be name convergence in Global Pathogen Analysis internet things: You can have GPAS (service) or GPAP (platform): eit-pathogena.com or www.dtu.dk/english/news...

Seems like Bobby Kennedy Jr misunderstands placental mammal reproduction. Go figure.

Terrific new feature presented by @theo.io on @pathoplexus.org called SeqSets for generating DOIs for sequence subsets used in publications, that can then be tracked for impact via CrossRef that will allow data generators to track impact! #IMMEMXiV

Amid the concerning news of a new Ebola Zaire outbreak in DRC, teams on the ground have already managed to sample, sequence, and share data. This rapid turnaround is a testament to their commitment and capacity to respond. Read more: virological.org/t/the-16th-e... 1/7

@zachhensel.bsky.social and I have a new paper on the origin of SARS-CoV-2! 🧪 There are a lot of reviews on the topic already, so we tried to do something different: characterize "lab leak" scenarios, and directly address those on SARS-CoV-2's furin cleavage site.▫️1/9 doi.org/10.5802/crbi...

Go home Evolution you're drunk

🎉 New in August: Measles virus joins Pathoplexus! Following strong community support, we added MeV data submission (with Open & Restricted-Use options, as always) and powerful search & data access for MeV pathoplexus.org/measles/search 5/10

🗓 Pathoplexus turns ONE! 🎂🎉 In the past year we’ve grown from 4 pathogens to a truly global, community-driven platform for transparent, equitable & impactful pathogen sequence sharing. 📰 Read the full update: pathoplexus.org/news/2025-08... 1/10

BEAST X accelerates Bayesian phylogenetic and phylodynamic inference with enhanced scalability and geo spread modeling. #BEASTX #Phylodynamics #VirusEvolution 👤EVBC: Philippe Lemey 🔗

Not to belabor a "I told you so", but it's been clear for years that the whole "lab leak" discourse has absolutely nothing to do with a potential lab leak and everything to do with a broader anti-science agenda. I really, and truly, hope more scientists will realize this and take corrective action.

Dang I never thought it would be so extensive killedbygoogle.com

Our Faraday Discovery Fellowships are now open for applications. These prestigious long-term awards are designed to support mid-career research leaders to undertake high-quality, original research. Find out more now: #RSGrants royalsociety.org/grants/farad...

Good choice!

"On the one hand, we have a hypothesis underpinned by evidence, although imperfect, and on the other hand we have a hypothesis without evidence, although it might exist." Our latest editorial in advance of our August issue www.thelancet.com/journals/lan... #IDSky #ClinMicro #ViroSky #SARS-CoV-2

You’ve been badly misled over COVID origins theconversation.com/how-conspira...

Some great new features and updates from the awesome Pathoplexus project. This is a new open pathogen genome database that can provide access to your sequences under a use-restricted license but also feed directly in to INSDC (EBI, Genbank etc) when you are ready. pathoplexus.org/news/2025-07...

Can also read a paper about Beast X here: doi.org/10.1038/s415...

Rummaging in my desk drawer: here is a photo of M101 - the Pinwheel Galaxy taken in March 2022 (left) and another one taken on 6th June 2023 (right). Both taken from my garden. Can you spot supernova SN 2023ixf discovered by Koichi Itagaki on the 19th May that year? Exploded 21M years ago.

BEAST X v10.5.0 finally released – you can't just do beta releases forever. github.com/beast-dev/be... Details and instructions for installing on the BEAST website: beast.community

An RNA virus acquires a polybasic cleaveage site insertion in the glycoprotein after jumping host into a high-density farmed species? Where have we seen that happen before (other than the many times we have watched in happen in HPAI)?

Quick thread on the WHO's SAGO report on the origins of COVID-19, highlighting key points and even *new* data. Their summary is that a zoonotic origin of COVID-19 is best supported by available data. This is consistent with most scientific reviews and statements in the rest of the literature.

SAGO Report is out: 1️⃣ No new data in report 2️⃣ Not bioweapon, man-made, or engineered 3️⃣ All scientific evidence points to zoonosis 4️⃣ No evidence for lab leak 5️⃣ New evidence could swing the conclusion In other words, what we concluded in April, 2020. Five years later. share.google/4I8ac1DJMZOM...

Handy to keep up with the ICTV's changes to virus taxonomy and species names: taxonomy.onecodex.com/taxon/694009... vs: taxonomy.onecodex.com/taxon/694009... or taxonomy.onecodex.com/taxon/11676/... vs taxonomy.onecodex.com/taxon/11676/...

Ever had to pause genomic surveillance due to enzyme shortages?🫣 Happy to share our new preprint with the solution inside 🦹‍♀️💪 biorxiv.org/content/10.110… @scalene.bsky.social @chris.primalscheme.com @pathogenomenick.bsky.social @articnetwork.bsky.social @nanoporetech.com

Wildlife trade acts as a vast global network of unregulated natural laboratories,with ample opportunities for viruses to circulate & evolve to become more dangerous We can either turn a blind eye or try to understand & mitigate the risks My latest in @nature.com 1/ www.nature.com/articles/d41...

Might be the time to finally make the switch from MacClade.

Ignoring mpox and its spread in African countries puts the whole world at risk. We have a vaccine that can effectively stop the outbreak but access in the parts of the world that need it most remains a challenge. We have to keep speaking about this. Thanks @kakape.bsky.social

An explosive outbreak of mpox in Sierra Leone is raising fears of wider spread. The country of 9 million has seen more than 3000 cases already. “We could see very rapid geographic expansion […] if we don’t really try and get things under control quickly,” says @kindrachukjason.bsky.social 🧪 #IDsky

Whether it comes to climate, AIDS denialism or the origin of SC2, Ridley’s ’gained function’ as a mouthpiece for the Tufton St MAGA alliance This isn’t a paper, it’s an opinion piece recycling ‘evidence’ that is either disputed by fact or conjecture based on cherry picking rumor to fit a conclusion

You might be wondering why we haven't updated outbreak.info for months. Well, the reason is that GISAID cut our access in January - as they did others. Without telling us. After a ♾️ back and forth, that is now permanent. More on that soon - and why GISAID should not be trusted with critical data.

Amazing work from our colleagues in Sierra Leone, Nigeria, and elsewhere, making the first sequences available from the ongoing Mpox epidemic in Sierra Leone. More to come - for now, head over to @pathoplexus.org: pathoplexus.org/seqsets/PP_S...

A long thread about mpox and the context specific nature of outbreaks prompted by the large outbreak of MPXV Clade IIb happening at the moment in Sierra Leone:

Sooo happy to finally have this one published!! (3 years in the making… 👀) A comprehensive investigation into the recency and geographical origins of both SARS-CoVs that spilled to humans in the past few decades, now in @cp-cell.bsky.social www.cell.com/cell/fulltex...

Interesting looking set of talks on 'What turns spillovers into epidemics?' w @jessmetcalf.bsky.social @danielstreicker.bsky.social @aineotoole.bsky.social @peacockflu.bsky.social @HouriyahTegally - 19th May www.oxfordmartin.ox.ac.uk/events/what-...

Viruses names are getting confusing w ongoing discussion in the community. From ICTV: Virus species names have been standardized; virus names remain unchanged 👉 journals.asm.org/doi/full/10.... Probably a response to: ‘Silly and pompous’: Official ne... 👉 www.science.org/content/arti...

University of Edinburgh #UoE near the top of another league table! www.timeshighereducation.com/news/uk-univ...

Starting now

Thanks to @lancetmicrobe.bsky.social for featuring our mSCAPE metagenomics surveillance collaboration and also thanks for the considered comments from Mario Falchi and Judy Breuer: www.thelancet.com/journals/lan... - keep an eye out on mSCAPE.climb.ac.uk for further details and resources

A heavily redacted Jan 2023 assessment by the US National Intelligence Council was just made public via FOIA. It contains the confirmation that, while leaning lab leak, the Department of Energy was not considering the Wuhan Institute of Virology as the source. www.documentcloud.org/documents/25...

🗓️ Pathoplexus has now been around for 7 months! And both we and our users have been busy - so we wanted to share some updates & highlights! 📰 You can see our full News Item here: pathoplexus.org/news/2025-04-16-spring-update 1/9

There have been many lab leak articles in the media recently, but none had actual new data In a new preprint, @zachhensel.bsky.social and I analyze early COVID-19 cases sequence data that have been overlooked so far. These new data continue to point to a natural origin ▫️1/7 doi.org/10.1101/2025...

An updated dataset of early SARS-CoV-2 diversity supports a wildlife market origin https://www.biorxiv.org/content/10.1101/2025.04.05.647275v1

Doesn’t look like T Coronae Borealis has exploded yet:

Have said before that conference organisers when deciding on a host country should consider how easy it is for people to get visas (particularly for those from the Global South). For example, applying for a Canadian visa from the UK takes 344 days (www.canada.ca/en/immigrati...).