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.

32610

Dr Emma Hodcroft @firefoxx66.bsky.social · 20/09/2026

Unfortunately "traffic-free" has failed a bit this time - unsure what's going on!

120

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! 🎂

13212

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

2167

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.

0155

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]

1155

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

1159

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.

01510

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

083

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.

2185

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!

2419

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.”

36613

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."

2424

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

1114

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.

1417

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

12613

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...

8704252

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!

1125

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

4545251094

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.

161300428

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

033

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.

02914

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.

33117

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

I'm not aware of such work - but I am not an expert in structure (it's not my field), so it may be ongoing

130

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

I hadn't thought of that! 🟧 Unfortunately may change in future as I just pick from a colour rainbow to cover all countries...!

000

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...

25428

Dr Emma Hodcroft @firefoxx66.bsky.social · 11/05/2026

And now they've been replaced by the Genbank sequence of the same sample from Switzerland. Early days are always a little messy - we appreciate the patience while we get it all organized! 😁

050

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.

09734

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)

212040

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.

05214

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.

1103

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

18339

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

It's always a bit of a balance being fully virologically correct and people knowing what you're talking about. For public social media posts like this I usually lean into trying to use terms people are more familiar with.

130

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

Bonus: See some tanglegrams (how similiar the phylogenies are between segments) between L & S nextstrain.org/groups/hodcr... And S & M nextstrain.org/groups/hodcr... Why don't some sequences have partners? There isn't always samples of all 3 segments - sometimes just 1 or 2.

0190

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...

56623

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

9478204

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. >

1258

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

050

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): 🧪

916361

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

Who else can you follow? As usual, @kakape.bsky.social is on it! Check out his great threads :) Or Science: www.science.org/content/arti... 9/N

1101

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

👀What will I be looking out for? I'll be interested to hear more about the contact patterns of those who've tested positive, and any further cases. The level of contact will be important to help us better understand what the level of H2H is & how spread happened. 8/N

182

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

🤒Importantly, it is possible we'll hear about more cases. Remember that hearing about more cases now doesn't necessarily mean it's spreading now that quarantine actions are in place - that long incubation means it's likely transmission happened earlier & is detected now. 7/N

1101

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

🧠So what's this mean? Possibly, we'll learn Hantavirus (at least Andes variant) has a higher H2H potential than previously thought. However, it still seems unlikely this will change the dynamics we have been observing in Hantavirus cases in general (not much H2H on land). 6/N

261

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

(And indeed, one of the crew cases seems to be a ship's doctor.) In short: ships have historically been fantastic places to spread infections in ways that are different (and worse) to dry land. 🛳️🦠🦠🦠 5/N

1133

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

Also, ships are very different from other environments - esp a small ship. 🛳️ These are close places - people share elevators, gyms, small rooms, meals. Unlike at home, if you're feeling ill you may continue to go to meals. People continue to clean your room. Doctors visit. 4/N

151

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

🤷🏻‍♀️So why am I not worried? Well, Hantaviruses cases aren't common, and the incubation period is long (1-8 wks). We may have previously underestimated H2H b/c by the time cases are detected, it's hard to tell if it was common exposure or H2H (esp if they live/work together). 3/N

151

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

🤔Why is it getting so much attention? Generally, human-to-human (H2H) transmission seems not so common in Hantavirus. Most cases are linked to direct exposure to rodent urine/feces/saliva. But on Hondius, it seems like H2H has very possibly taken place on the ship. 2/N

151

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

1409

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

I mean it keeps the organs in though? And mostly keeps the rain out. Points for that!

160