In light of the ongoing situation with Ebola in the DRC, I'm sorry to have to remind you that evolutionary biology makes it abundantly clear that ignoring a catastrophic disease outbreak because it's there, not here, is a terrible, terrible idea.

Looking to find out more about genomic epidemiology and Hantavirus/ANDV? I'll be chairing a excellent panel of experts tomorrow (alongside some great opening speakers) - stop by and hear what they have to say!

Birth rate discourse is like “It turns out if you give women more choices, they’re less likely to make ones that make their lives harder.” Which is really helpful in figuring out how we can improve society somewhat. But instead people are like wow giving women more choices was a mistake

The contrast between the number of media requests I got when rich people on a cruise were facing a deadly, but contained outbreak versus now that some of the poorest people in the world are facing a deadly and devastating epidemic is just so so stark and it just really annoys the hell out of me.

🚨 Hantavirus and genomic epidemiology: Has it been smooth sailing? Join a special PHA4GE & IPSN webinar exploring how genomics supported the response to the Hantavirus outbreak. 📅 20 May 2026 🕒 14:00 CEST 📍 Zoom Register: bit.ly/4ulwHKm #PHA4GE #Hantavirus

Teams in the Democratic Republic of the Congo & Uganda have now shared the first sequences from the current Ebola (Bundibugyo virus) outbreak using Pathoplexus, just days after cases were confirmed. Read more about the response to Bundibugyo virus here: pathoplexus.org/news/2026-05...

1/ 🚀 Pathoplexus now supports Bundibugyo virus (BDBV), a species of Ebolavirus. BDBV has been associated with past outbreaks of Ebola in the DR Congo and Uganda, & a case has been reported today during response to the current Ebola outbreak. pathoplexus.org/ebola-bdbv #ebola #bdbv #ebolaoutbreak

Nextstrain #ANDV trees updated with a few improvements: - 2 outbreaks marked - host scientific/common name added - province now visible on map - date colouring added Here's a quick tour of how to change colours, geography & names! Links to trees here (scroll down): nextstrain.org/groups/hodcr...

Since launching support for the Andes virus species of hantavirus two days ago, we have already received submissions from four countries' sequencing teams. This is a testament to the rapid response of researchers, sharing real-time data. Read more in our news post: pathoplexus.org/news/2026-05...

My ANDV #Hantavirus @nextstrain.org phylogenies now pull directly from @pathoplexus.org to incorporate all seqs I'll continue to improve them, & will keep them updated Change the Tip Labels in the left-hand menu. You can see links to all builds, plus tanglegrams at: nextstrain.org/groups/hodcr...

Incredibly proud of the @pathoplexus.org team for getting this up so quickly. In an outbreak like this, it's critical to share data quickly & openly - so scientists can do public health analyses (like the @nextstrain.org builds) - while still protecting the right to publish on generated sequences.

4/ This is an ongoing outbreak of high interest, with few sequences available. In such a situation, Restricted-Use sequences are highly unlikely to be ‘background’ sequences. Please ensure you follow our Data Use Terms in preprints/publications & co-author with other submitters.

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

I've built some initial Nextstrain phylogenies of the Andes Hantavirus variant, which include the sequence generated by HUG & UniZurich, Switzerland. Please interpret with caution. By segment: S: nextstrain.org/groups/hodcr... M: nextstrain.org/groups/hodcr... L: nextstrain.org/groups/hodcr...

After 15 years of reporting on infectious disease outbreaks, what continues to fascinate me about them is the challenge of making high-stakes decisions under uncertainty. The hantavirus outbreak on the MV Hondius is a perfect example My story in @science.org is here (and a thread to come): 🧪 #IDsky

A useful concept in outbreaks is the "reasonable worst case", which is not the worst that can happen but is significantly worse than the current trajectory. The current trajectory is that this is a very distressing situation for those involved that we can take meaningful steps to avoid in future. >

📢EVE Group is thrilled to announce the 1st Swiss Enterovirus Symposium🦠, this autumn in beautiful Disentis! Registration opens soon - but go ahead and - 📑 submit your abstract: forms.gle/Jfh86NqncGpy... - 💵 apply for a student travel grant: forms.gle/6GzLKQZoUzu4... ! 🏔️ See you there! ses2026.org

Probably a good time for a few general caveats for those watching the developing story of the #hantavirus outbreak linked to the cruise ship MV Hondius - especially the more anxious ones among you. (Long-time followers will know most of this by heart at this point): 🧪

I've had a lot of questions about Hantavirus recently - and some alarmism in some places. It's been a while since I wore this hat - but let's chat! 💬 Top Line: Am I worried? No, not really. I don't see evidence this is something that will spread widely. 1/N

More days like this please

I'm not a religious person, but I've been more interested in the old biblical stories since I really realised just how radical it is to tell people "do not kill."

Why not let a perfectly functional device just keep functioning? 😠

Second day of #gfv2026 starting off with fantastic plenary talks by Nihal Altan-Bonnet, Paul Lehner and Emma Hodcroft @firefoxx66.bsky.social 🤩

If you want to join a team making pathogen sequencing and analysis for public health, surveillance, and research more accessible, more equitable and more ✨awesome✨ - look no further - come join us on this mission at ARTIC! #openscience #opendata #opensource

ARTIC are hiring! Postdoctoral opportunity in metagenomics at the University of Birmingham edzz.fa.em3.oraclecloud.com/hcmUI/Candid...

1/ 🦟 Big news: #Pathoplexus now supports Dengue virus & Yellow Fever virus - two arboviruses responsible for over 400 million infections and up to 94,000 deaths per year. Here's what’s new in our latest update 👇🏻 Read the full update: pathoplexus.org/news/2026-03... 📰

1/5 Introducing SimPlot-CL! 🧬 Recombination plays an important role in viral evolution. Similarity plots are a great way to visualize recombination patterns, but generating them across many genomes can be cumbersome (Work with my student, Keno Strotjohann!) 📂 github.com/hodcroftlab/simplot-cl

In 2025, GISAID cut off access to many critical SARS-CoV-2 resources, incl. our outbreak.info. A month ago, GISAID leveled accusations against us, Cov-Spectrum, Nextstrain, and members of COG-UK, which are false and misrepresent known facts. Our joint response: blog.outbreak.info/joint-respon...

From Basel #Fastnacht 2026

Looking forward to the #SocialMediaCafe for researchers tomorrow tue, 25.2.2026, 12.15-13h with guest @firefoxx66.bsky.social. We will talk about the use of social media for researchers and focus on Bluesky. The cafe is open to all ZHAW-researchers. Check the intranet: intra.zhaw.ch/departemente...

Every year I get to 're-live' the pandemic thanks to FB memories. Re-examining my posts with increasing time is always interesting. This one though - this one never fails to send a shiver down my spine. When do make a post like this? When are you sure enough? What if you regret it?

Invited speaker Emma Hodcroft @firefoxx66.bsky.social presenting Pathoplexus and the readyness to respond in the @lifesciswitzerland.bsky.social #LS2AM symposium of the @sib.swiss Bioinformatics Section.

Highlighting the speaker who stood in front of the Surprise mayor and told him to consider what the Mayor of Ohrdruf must’ve thought before he died by suicide: “He might have thought ‘how is this my fault I had no jurisdiction over this’ maybe he said ‘this site was not subject to local zoning.’”

Just a reminder - if you're in Zurich tonight and interested in open data sharing, come hear me speak at 18.00! (Only 20 minutes, in English!)

In Zurich on Monday evening? Want to hear about #opendata & data sharing, and how critical it is for preparing for and responding to infectious diseases? 🔓🧬 Come hear me speak at Karl de Grosse Debattierhaus Winterreden! 🪟💬 👉🏻 19 Jan, 18.00, 20 mins, English www.karldergrosse.ch/programm/ver...

In Zurich on Monday evening? Want to hear about #opendata & data sharing, and how critical it is for preparing for and responding to infectious diseases? 🔓🧬 Come hear me speak at Karl de Grosse Debattierhaus Winterreden! 🪟💬 👉🏻 19 Jan, 18.00, 20 mins, English www.karldergrosse.ch/programm/ver...

Sigh. For the hundredth time, we are not judging his character, we are judging his actions. The RS position would be fine if it was a gentlemen's club, who can have who it damn well pleases. But it positions itself as represnting British science and scientists. Now an embarrassment, to be frank.

This needs boosting. How we share data now, determines how prepared we are for tomorrow. That includes having access to *all* who need it (inccitizen scientists like @ryanhisner.bsky.social) & being able to use it in dashboards & apps. Having one place control it all - is dangerous. #OpenScience

POV, you need to be out of the rental house by 11am tomorrow, so all hands on deck to finish the Christmas Puzzle! Wishing you all a joyful and merry Christmas, full of puzzles and loved ones! 🎁🎄☃️

Best Christmas Card of 2025 award goes out to the @biozentrum.unibas.ch for this incredible building-themed-advent-calendar! Opening a window each day has been fantastic! ❄️☃️😁

Oh my god they found poisson steve #poissonsteve

1/ 🚀 Pathoplexus now supports Marburg virus (MARV) and Ravn virus (RAVN) (sister viruses in the same genus). MARV has two main clades and causes severe disease with reported fatality rates of 24–88%. You can read more detail about adding Marburg here: pathoplexus.org/news/2025-11...

The change to the CDC website to reflect unscientific, agenda-driven mindsets is deeply upsetting. But let's not forget there are a lot of excellent scientists still working there. Persisting. Trying to minimise damage. Let's not stop supporting them - while condemning those in charge!

1/ 🚀 Exciting news: we’ve just released the first Nextclade dataset for Enterovirus D68 (EV-D68), developed in collaboration with the European Non-Polio Enterovirus Network (ENPEN). 👉🏻 Check out the dataset on Nextclade! clades.nextstrain.org?dataset-name... #EVD68 #Enterovirus #OpenData

1/ 🚀 Big thanks to our community - since August we’ve added thousands of new sequences, rolled out major new features, and welcomed fresh faces into the #Pathoplexus world. Let’s dive into what’s new.👇🏻 Read the full update: pathoplexus.org/news/2025-11...

Looking forward to sharing @pathoplexus.org next week at the @evbc.bsky.social Viruses in Silico lecture! Tune in if you'd like to hear about open but protected data sharing, simple uploads, & transparent governance - all to help with easier, faster viral genome sharing! #opendata #openscience

📢 Next Viruses in silico lecture: 🎙️ Pathoplexus: A Community-Driven Solution for Transparent and Equitable Viral Genomic Data Sharing 👩‍🔬 Emma Hodcroft @firefoxx66.bsky.social (@swisstph.ch @sib.swiss) 🗓️ 27 Nov 2025 🕑 4 PM CET 📍 Zoom - Register to receive login details 👉 tinyurl.com/VirInSilico

Open position at the Swiss Institute of Bioinformatics: We are looking for a Director of the Center of Pathogen Bioinformatics apply.refline.ch/499599/0346/... I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and

I want to spell this out in case the implications aren't clear: This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited. The file allowed this. Cut that - cut off all tools the public & others were using.

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