iiinova — where your digital self keeps evolving

Reposted by Dr Emma Hodcroft

Pathoplexus @pathoplexus.org · 22/09/2026

1/ 🧬 A big #Pathoplexus milestone: you can now optionally include raw sequencing reads alongside your consensus sequences! Hosting raw reads alongside consensus data helps improve reproducibility & allow in-depth analyses. 📰 Read more: pathoplexus.org/news/2026-09...

AI-generated image showing raw reads (short reads) lining up above a consensus sequence, with both the raw reads and consensus sequence labelled. Vague images below show a virus, coverage, and DNA.

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Dr Emma Hodcroft @firefoxx66.bsky.social · 27/08/2026

I'm so incredibly proud of what we've built in these past two years! But I also can't wait to see what comes next - we've still got so much more do to! Happy Birthday Pathoplexus! 🎂

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Reposted by Dr Emma Hodcroft

Pathoplexus @pathoplexus.org · 26/08/2026

1/ 🦟 New on @Pathoplexus: Zika virus (ZIKV) is now supported! Share your ZIKV sequences as Open or Restricted-Use, just like our other pathogens. Read more: pathoplexus.org/news/2026-08... 📰

Screenshot of the Pathoplexus website homepage, where the new Zika virus button is circled in red

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Reposted by Dr Emma Hodcroft

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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Reposted by Dr Emma Hodcroft

Theo Sanderson @theo.io · 23/07/2026

I'm really excited about SeqSets reaching fruition. Sequencing pathogen genomes is impactful: this data enables us to design vaccines, to predict future evolution, and more. But at the moment, getting scientific credit mostly requires writing a paper, not just sequencing a genome. [1/n]

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Reposted by Dr Emma Hodcroft

Pathoplexus @pathoplexus.org · 23/07/2026

1/ 🛠️ Our July update is here - and it's a technical one! New features for citations, search, submission, and more. Here's what's new in #Pathoplexus 👇 🔗 Full post: pathoplexus.org/news/2026-07...

Screenshot of the Pathoplexus website homepage

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Reposted by Dr Emma Hodcroft

ARTIC network @artic.network · 01/07/2026

Important read from ARTIC PI Placide Mbala (INRB) and @krutikakuppalli.bsky.social in @statnews.com, on what the Bundibugyo Ebola outbreak reveals about the limits of pathogen-specific diagnostics, and why we need pathogen-agnostic systems for the next emergency www.statnews.com/2026/07/01/e...

statnews.com

What Ebola and Marburg are teaching us about the next pandemic

“What is urgently needed is a shift from pathogen-specific diagnostics toward pathogen-agnostic diagnostic systems,” write Krutika Kuppalli and Placide Mbala.

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Reposted by Dr Emma Hodcroft

Pathoplexus @pathoplexus.org · 01/07/2026

Our first Annual Report is here! 📊 Covering Aug 2024 (our founding) through 2025: new viruses added, global submissions, software upgrades, & community & governance milestones. True to our values, it includes a full financial report + an audit 🔗 pathoplexus.org/about/govern...

Screenshot of the first page of the pathoplexus annual report 2024-2025, which includes the first few lines of the report, describing the founding of Pathoplexus in August 2024

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Reposted by Dr Emma Hodcroft

Pathoplexus @pathoplexus.org · 30/06/2026

1/ 🌍 Our June update is here! Two new pathogens added in response to active outbreaks, over 5,700 new sequences, and a growing community of labs from around the world. Here's what's new in #Pathoplexus 👇 Read the full update: pathoplexus.org/news/2026-06... 📰

A screenshot of all supported viruses on the Pathoplexus front page, with ANDV and BDBV highlighted.

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Dr Emma Hodcroft @firefoxx66.bsky.social · 24/06/2026

Studies have shown that sleep deprivation can be equal to the effects of drinking alcohol for reaction time & attentiveness. For multiple nights now, many Basel residents won't have slept well in extreme heat - but may still be driving or operating machines. Be safe in this extreme heat everyone!

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Reposted by Dr Emma Hodcroft

Kai Kupferschmidt @kakape.bsky.social · 14/06/2026

“By the way, they even said, OK, you invest a lot of money, and you know, even senior people come to us when Ebola comes. But you’re coming to prevent Ebola from coming to you to stop it here. It’s not because you want to save our lives. It’s not for us, it’s for you.”

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Dr Emma Hodcroft @firefoxx66.bsky.social · 19/06/2026

The 11th commandment is actually "Thou shalt not send back an edited document with the same file name as the original."

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Dr Emma Hodcroft @firefoxx66.bsky.social · 18/06/2026

📢Final days for abstracts/grants- deadline 22 Jun! Join us for the 1st Swiss Enterovirus Symposium, this Oct in Disentis! - 📑 submit abstract: forms.gle/Jfh86NqncGpy... - 💵 apply for student travel grant: forms.gle/6GzLKQZoUzu4... - 🎫 register: www.sib.swiss/event-coordi... 🏔️ More: ses2026.org

Banner for the 1st Swiss Enterovirus Symposium 2026. Shows a virus to the left and a picture of a monastery in the Alps on the right. Tagline says: "Enterovirus Research and Surveillance: Strengthening Networks in Europe and Beyond".
Dates: 5-8 October 2026
Location: Disentis, Switzerland
Information: In-person only
Website: ses2026.org

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Dr Emma Hodcroft @firefoxx66.bsky.social · 08/06/2026

If you transitted through Vienna today and are missing a green suitcase, I can report that it's enjoying the sun on the tarmac outside of Gate 61. Hope it finds you again!

Photo of a lone green rolling suitcase sitting completely alone in the middle of a busy airport gate area tarmac surrounded by aircraft stairs and airport vehicles, in the sun.

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Reposted by Dr Emma Hodcroft

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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Reposted by Dr Emma Hodcroft

Carl T. Bergstrom @carlbergstrom.com · 28/05/2026

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.

thelancet.com

Evolutionary consequences of delaying intervention for monkeypox

Since May, 2022, clusters of monkeypox infections have caused global concern. At present, this concern has been tempered by the fact that, even when uncontrolled, the number of infections is growing s...

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Dr Emma Hodcroft @firefoxx66.bsky.social · 19/05/2026

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!

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Reposted by Dr Emma Hodcroft

Kat Tenbarge @kattenbarge.bsky.social · 17/05/2026

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

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Reposted by Dr Emma Hodcroft

Kai Kupferschmidt @kakape.bsky.social · 19/05/2026

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.

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Reposted by Dr Emma Hodcroft

pha4ge.bsky.social @pha4ge.bsky.social · 18/05/2026

🚨 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

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Reposted by Dr Emma Hodcroft

Pathoplexus @pathoplexus.org · 19/05/2026

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...

pathoplexus.org

Pathoplexus | Ebola: Rapid response to the Bundibugyo virus outbreak in the DRC and Uganda

Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

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Reposted by Dr Emma Hodcroft

Pathoplexus @pathoplexus.org · 15/05/2026

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

Image of some of the available pathogens on Pathoplexus, with a red rectangle outlining the new tile for Ebola Bundibugyo virus, with 44 sequences.

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Dr Emma Hodcroft @firefoxx66.bsky.social · 14/05/2026

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...

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Reposted by Dr Emma Hodcroft

Pathoplexus @pathoplexus.org · 11/05/2026

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...

pathoplexus.org

Pathoplexus | Andes virus: supporting response to the current hantavirus outbreak

Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

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Dr Emma Hodcroft @firefoxx66.bsky.social · 10/05/2026

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...

A phylogenetic tree showing linked sequences from the S and L segment of ANDV virus (Andes Hantavirus)

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Dr Emma Hodcroft @firefoxx66.bsky.social · 09/05/2026

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.

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Reposted by Dr Emma Hodcroft

Pathoplexus @pathoplexus.org · 09/05/2026

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.

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Reposted by Dr Emma Hodcroft

Pathoplexus @pathoplexus.org · 09/05/2026

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

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Dr Emma Hodcroft @firefoxx66.bsky.social · 08/05/2026

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...

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Reposted by Dr Emma Hodcroft

Kai Kupferschmidt @kakape.bsky.social · 08/05/2026

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

science.org

What to do with the passengers on the cruise ship hit by hantavirus?

Past studies of Andes virus offer scant evidence on transmission risks, and have sparked debate

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Reposted by Dr Emma Hodcroft

Thomas House @tah-sci.com · 08/05/2026

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. >

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Dr Emma Hodcroft @firefoxx66.bsky.social · 07/05/2026

📢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

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Reposted by Dr Emma Hodcroft

Kai Kupferschmidt @kakape.bsky.social · 06/05/2026

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): 🧪

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Dr Emma Hodcroft @firefoxx66.bsky.social · 06/05/2026

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

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Dr Emma Hodcroft @firefoxx66.bsky.social · 18/04/2026

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."

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Dr Emma Hodcroft @firefoxx66.bsky.social · 08/04/2026

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

Email from amazon announcing they will no longer support Kindle devices from 2012 or earlier - even if they are working fine.

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Reposted by Dr Emma Hodcroft

GfV - Gesellschaft für Virologie @gesvirologie.bsky.social · 18/03/2026

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

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Dr Emma Hodcroft @firefoxx66.bsky.social · 12/03/2026

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

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Reposted by Dr Emma Hodcroft

Pathoplexus @pathoplexus.org · 12/03/2026

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... 📰

A screenshot of the new Pathoplexus homepage showing all viruses now supported, including Dengue and Yellow Fever, which are circled in red

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Dr Emma Hodcroft @firefoxx66.bsky.social · 10/03/2026

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

A figure showing a 'Simplot' which plots the similarity of a genome to other genomes across a graph, with similarity on the Y-axis and the genome position on the x-axis. Many coloured lines show the sequences being compared - those closest to the top (similarity of 1) are the closest matches in different parts of the genome.

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Reposted by Dr Emma Hodcroft

Kristian G. Andersen @kgandersen.bsky.social · 24/02/2026

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...

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Philipp Funk @philippfunk.bsky.social · 24/02/2026

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...

intra.zhaw.ch

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Dr Emma Hodcroft @firefoxx66.bsky.social · 23/02/2026

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?

A screenshot of a FB memories post from 6 years ago today, 23 Feb 2020. Emma Hodcroft posts: "So yea. This is it. This is the post.
SARS-CoV-2 is extremely likely to become (if not already) pandemic.
What's most important right now is getting a handle on how quickly it is spreading and where.
This means increasing testing and trying to slow the spread to buy time."

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Reposted by Dr Emma Hodcroft

Katja @jaggakatja.bsky.social · 12/02/2026

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.

Emma Hodcroft presenting Pathoplexus at the LS2 Annual Meeting

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Reposted by Dr Emma Hodcroft

Arizona Right Watch @azrww.bsky.social · 04/02/2026

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.’”

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Dr Emma Hodcroft @firefoxx66.bsky.social · 19/01/2026

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!)

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