Collins Tanui et al. reporten una estimació filodinàmica del nombre reproductiu del brot de virus Ebola-Bundibugyo.
virological.org/t/reproducti...
virological.org/t/reproducti...
Reproduction number of the 2026 Bundibugyo virus disease outbreak over time: phylodynamic estimates from genomes collected up to 5 October 2026
This post adheres to Policy and guidelines on the use of generative AI models in posts on Virological.org on the use of generative AI models. This analysis reflects the Pathoplexus database state of ...
virological.org
October 23, 2026 at 3:50 PM
Collins Tanui et al. reporten una estimació filodinàmica del nombre reproductiu del brot de virus Ebola-Bundibugyo.
virological.org/t/reproducti...
virological.org/t/reproducti...
This is a big deal for virus data sharing. Submitters can now upload raw reads, immediately share them with collaborators, and let Pathoplexus take care of the INSDC submission process on their behalf…
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...
Hosting raw reads alongside consensus data helps improve reproducibility & allow in-depth analyses.
📰 Read more: pathoplexus.org/news/2026-09...
September 23, 2026 at 1:06 PM
This is a big deal for virus data sharing. Submitters can now upload raw reads, immediately share them with collaborators, and let Pathoplexus take care of the INSDC submission process on their behalf…
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...
Hosting raw reads alongside consensus data helps improve reproducibility & allow in-depth analyses.
📰 Read more: pathoplexus.org/news/2026-09...
September 22, 2026 at 8:06 PM
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...
Hosting raw reads alongside consensus data helps improve reproducibility & allow in-depth analyses.
📰 Read more: pathoplexus.org/news/2026-09...
2/ ⚙️ How it works: raw reads follow all the same policies as consensus sequences - your chosen Data Use Terms apply to both, and raw reads are openly downloadable as soon as processing completes.
Pathoplexus handles INSDC submission for you, just like today.
Pathoplexus handles INSDC submission for you, just like today.
September 22, 2026 at 8:06 PM
2/ ⚙️ How it works: raw reads follow all the same policies as consensus sequences - your chosen Data Use Terms apply to both, and raw reads are openly downloadable as soon as processing completes.
Pathoplexus handles INSDC submission for you, just like today.
Pathoplexus handles INSDC submission for you, just like today.
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! 🎂
But I also can't wait to see what comes next - we've still got so much more do to!
Happy Birthday Pathoplexus! 🎂
1/ 🎂 Pathoplexus turns TWO! 🎉
Two years ago we launched with an idea: what if pathogen data sharing put open access, speed, ease of use, & credit for data generators at its center? Here's what our community has built since:
📰 Read the full update: pathoplexus.org/news/2026-08...
Two years ago we launched with an idea: what if pathogen data sharing put open access, speed, ease of use, & credit for data generators at its center? Here's what our community has built since:
📰 Read the full update: pathoplexus.org/news/2026-08...
August 27, 2026 at 3:51 PM
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! 🎂
But I also can't wait to see what comes next - we've still got so much more do to!
Happy Birthday Pathoplexus! 🎂
7/ 🦟 And just this week: Zika virus joined Pathoplexus, our newest addition!
bsky.app/profile/path...
bsky.app/profile/path...
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... 📰
Read more: pathoplexus.org/news/2026-08... 📰
August 27, 2026 at 3:42 PM
7/ 🦟 And just this week: Zika virus joined Pathoplexus, our newest addition!
bsky.app/profile/path...
bsky.app/profile/path...
9/ ❤️ To everyone who's submitted a sequence, flagged a curation issue, joined our Scientific Advisory Board, presented a poster, funded our work, or told a colleague about us - thank you.
2️⃣ Here's to year two, and many more to come! 🎊
🔗 Full post: pathoplexus.org/news/2026-08...
2️⃣ Here's to year two, and many more to come! 🎊
🔗 Full post: pathoplexus.org/news/2026-08...
Pathoplexus | Pathoplexus Turns Two
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.
pathoplexus.org
August 27, 2026 at 3:42 PM
9/ ❤️ To everyone who's submitted a sequence, flagged a curation issue, joined our Scientific Advisory Board, presented a poster, funded our work, or told a colleague about us - thank you.
2️⃣ Here's to year two, and many more to come! 🎊
🔗 Full post: pathoplexus.org/news/2026-08...
2️⃣ Here's to year two, and many more to come! 🎊
🔗 Full post: pathoplexus.org/news/2026-08...
8/ 🙏 None of this happens on its own. Thank you to our Executive Board, our members who guide and hold us accountable, our developer team, and every researcher, lab, and institute who has chosen to share data through Pathoplexus.
August 27, 2026 at 3:42 PM
8/ 🙏 None of this happens on its own. Thank you to our Executive Board, our members who guide and hold us accountable, our developer team, and every researcher, lab, and institute who has chosen to share data through Pathoplexus.
1/ 🎂 Pathoplexus turns TWO! 🎉
Two years ago we launched with an idea: what if pathogen data sharing put open access, speed, ease of use, & credit for data generators at its center? Here's what our community has built since:
📰 Read the full update: pathoplexus.org/news/2026-08...
Two years ago we launched with an idea: what if pathogen data sharing put open access, speed, ease of use, & credit for data generators at its center? Here's what our community has built since:
📰 Read the full update: pathoplexus.org/news/2026-08...
August 27, 2026 at 3:42 PM
1/ 🎂 Pathoplexus turns TWO! 🎉
Two years ago we launched with an idea: what if pathogen data sharing put open access, speed, ease of use, & credit for data generators at its center? Here's what our community has built since:
📰 Read the full update: pathoplexus.org/news/2026-08...
Two years ago we launched with an idea: what if pathogen data sharing put open access, speed, ease of use, & credit for data generators at its center? Here's what our community has built since:
📰 Read the full update: pathoplexus.org/news/2026-08...
4/ 🧬 Steady, ongoing sharing across our pathogens:
- Dengue (3,557)
- Mpox (3,686)
- RSV-A (3,618)
- RSV-B (3,653)
- Measles (1,908)
- West Nile (993)
- BDBV (648)
- HMPV (488)
- Ebola Zaire (72) - plus critical additions to ANDV, Marburg, CCHF, Yellow Fever & Ebola Sudan.
- Dengue (3,557)
- Mpox (3,686)
- RSV-A (3,618)
- RSV-B (3,653)
- Measles (1,908)
- West Nile (993)
- BDBV (648)
- HMPV (488)
- Ebola Zaire (72) - plus critical additions to ANDV, Marburg, CCHF, Yellow Fever & Ebola Sudan.
August 27, 2026 at 3:42 PM
4/ 🧬 Steady, ongoing sharing across our pathogens:
- Dengue (3,557)
- Mpox (3,686)
- RSV-A (3,618)
- RSV-B (3,653)
- Measles (1,908)
- West Nile (993)
- BDBV (648)
- HMPV (488)
- Ebola Zaire (72) - plus critical additions to ANDV, Marburg, CCHF, Yellow Fever & Ebola Sudan.
- Dengue (3,557)
- Mpox (3,686)
- RSV-A (3,618)
- RSV-B (3,653)
- Measles (1,908)
- West Nile (993)
- BDBV (648)
- HMPV (488)
- Ebola Zaire (72) - plus critical additions to ANDV, Marburg, CCHF, Yellow Fever & Ebola Sudan.
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... 📰
Read more: pathoplexus.org/news/2026-08... 📰
August 26, 2026 at 2:34 PM
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... 📰
Read more: pathoplexus.org/news/2026-08... 📰
2/ 🧬 ZIKV often causes mild or no symptoms - but can rarely lead to Guillain-Barré syndrome or birth defects, making surveillance important.
🙏 Thanks to Arthur Shem Kasambula for leading this addition, & as always, to our submitters, curators, & community for helping expand Pathoplexus!
🙏 Thanks to Arthur Shem Kasambula for leading this addition, & as always, to our submitters, curators, & community for helping expand Pathoplexus!
August 26, 2026 at 2:34 PM
2/ 🧬 ZIKV often causes mild or no symptoms - but can rarely lead to Guillain-Barré syndrome or birth defects, making surveillance important.
🙏 Thanks to Arthur Shem Kasambula for leading this addition, & as always, to our submitters, curators, & community for helping expand Pathoplexus!
🙏 Thanks to Arthur Shem Kasambula for leading this addition, & as always, to our submitters, curators, & community for helping expand Pathoplexus!
Auf Pathoplexus können Wissenschaftlerinnen und Wissenschaftler ihre Virusdaten für maximal ein Jahr schützen: Andere Forschungsgruppen können sofort darauf zugreifen und damit arbeiten, dürfen aber keine eigenen Publikationen damit veröffentlichen. 3/4
June 18, 2025 at 8:55 AM
Auf Pathoplexus können Wissenschaftlerinnen und Wissenschaftler ihre Virusdaten für maximal ein Jahr schützen: Andere Forschungsgruppen können sofort darauf zugreifen und damit arbeiten, dürfen aber keine eigenen Publikationen damit veröffentlichen. 3/4
Zu @firefoxx66.bsky.social: "...,das Fachjournal «Nature» @nature.com hat Sie zu einer von drei Personen gewählt, die 2025 die Wissenschaft besonders prägen werden."
Zu #Pathoplexus, "Wir haben mit unserer Plattform eine Lösung für ein Dilemma gefunden: Forschende teilen nämlich ungern Daten,
1/4
Zu #Pathoplexus, "Wir haben mit unserer Plattform eine Lösung für ein Dilemma gefunden: Forschende teilen nämlich ungern Daten,
1/4
I'm honoured to have been featured in @unibas.ch 's UniNova magazine! 🙏🙌
In my interview, I speak about the importance of @pathoplexus.org, what Enteroviruses can teach us, & the damage to science (& health) from the current US administration. [German]
www.unibas.ch/de/Aktuell/U...
In my interview, I speak about the importance of @pathoplexus.org, what Enteroviruses can teach us, & the damage to science (& health) from the current US administration. [German]
www.unibas.ch/de/Aktuell/U...
Gemeinsam forschen gegen die nächste Seuche.
Emma Hodcroft untersucht, wie unser Zusammenleben mit Viren die Krankheitserreger und uns verändert. Angesichts von Vogelgrippe, Ebola und Co. blickt sie mit Sorge auf den Kahlschlag der US-Regierung ...
www.unibas.ch
June 18, 2025 at 8:55 AM
Zu @firefoxx66.bsky.social: "...,das Fachjournal «Nature» @nature.com hat Sie zu einer von drei Personen gewählt, die 2025 die Wissenschaft besonders prägen werden."
Zu #Pathoplexus, "Wir haben mit unserer Plattform eine Lösung für ein Dilemma gefunden: Forschende teilen nämlich ungern Daten,
1/4
Zu #Pathoplexus, "Wir haben mit unserer Plattform eine Lösung für ein Dilemma gefunden: Forschende teilen nämlich ungern Daten,
1/4
If you are not following Pathoplexus @pathoplexus.org @firefoxx66.bsky.social please do!
It’s an excellent initiative, which will likely become increasingly important over time.
It’s an excellent initiative, which will likely become increasingly important over time.
It's an incredible honour to have received this #OpenData prize from Swiss Academies of Arts & Sciences for @pathoplexus.org!
Though not everyone in Pathoplexus could be there in person, it was a fantastic & thought-provoking event, & I'm so glad were part of it! #OpenScience #OpenSource
Though not everyone in Pathoplexus could be there in person, it was a fantastic & thought-provoking event, & I'm so glad were part of it! #OpenScience #OpenSource
November 28, 2024 at 5:41 PM
If you are not following Pathoplexus @pathoplexus.org @firefoxx66.bsky.social please do!
It’s an excellent initiative, which will likely become increasingly important over time.
It’s an excellent initiative, which will likely become increasingly important over time.
This initiative looks like it will become increasingly valuable moving forward.
See also recent Nature article
www.nature.com/articles/d41...
featuring @firefoxx66.bsky.social
See also recent Nature article
www.nature.com/articles/d41...
featuring @firefoxx66.bsky.social
September 11, 2024 at 8:23 AM
This initiative looks like it will become increasingly valuable moving forward.
See also recent Nature article
www.nature.com/articles/d41...
featuring @firefoxx66.bsky.social
See also recent Nature article
www.nature.com/articles/d41...
featuring @firefoxx66.bsky.social
Oh come on GISAID. And that's why we need data portals that are free and open - especially when it comes to monitoring pathogens with genomic data. Such as Pathoplexus (Awesome initiative! www.nature.com/articles/d41...).
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.
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.
May 30, 2025 at 10:08 AM
Oh come on GISAID. And that's why we need data portals that are free and open - especially when it comes to monitoring pathogens with genomic data. Such as Pathoplexus (Awesome initiative! www.nature.com/articles/d41...).
New virus-genome website seeks to make sharing sequences easy and fair www.nature.com/articles/d41...
New virus-genome website seeks to make sharing sequences easy and fair
The Pathoplexus database has sequences from Ebola, West Nile virus and another dangerous pathogen. The Pathoplexus database has sequences from Ebola, West Nile virus and another dangerous pathogen.
www.nature.com
September 9, 2024 at 1:52 PM
New virus-genome website seeks to make sharing sequences easy and fair www.nature.com/articles/d41...
Pathoplexus is growing not only in terms of new sequences, but also integrating into the larger ecosystem of pathogen surveillance by joining WHO's IPSN and expanding membership. This is the way a pathogen sequence database should work! (Lessons learned from GISAID/SARS-CoV-2...)
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...
Read the full update: pathoplexus.org/news/2025-11...
November 18, 2025 at 7:32 PM
Pathoplexus is growing not only in terms of new sequences, but also integrating into the larger ecosystem of pathogen surveillance by joining WHO's IPSN and expanding membership. This is the way a pathogen sequence database should work! (Lessons learned from GISAID/SARS-CoV-2...)
Fantastic opportunity in Switzerland for a post-doc or dev, working on open-source tools to support global pathogen sequencing efforts (ARTIC2) and data sharing with protections for contributor's first-publication rights (Pathoplexus). 🧵
📢New job posting!📢
Are you excited by the idea of building global infrastructure to make pathogen sequencing more accessible, interpretable, and equitable? 🧑🏻💻🧬
My group at @swisstph.ch has an opening working with ARTIC2, @pathoplexus.org, & Loculus - read on!
1/5
Are you excited by the idea of building global infrastructure to make pathogen sequencing more accessible, interpretable, and equitable? 🧑🏻💻🧬
My group at @swisstph.ch has an opening working with ARTIC2, @pathoplexus.org, & Loculus - read on!
1/5
July 25, 2025 at 11:39 PM
Fantastic opportunity in Switzerland for a post-doc or dev, working on open-source tools to support global pathogen sequencing efforts (ARTIC2) and data sharing with protections for contributor's first-publication rights (Pathoplexus). 🧵
Congrats to Pathoplexus and sequence contributors!
🗓️ 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
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
Pathoplexus | Pathoplexus Spring Update
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.
pathoplexus.org
April 16, 2025 at 4:39 PM
Congrats to Pathoplexus and sequence contributors!
The Lord’s work. Congrats to Emma Hodcroft and all involved. May Pathoplexus quickly supplant GISAID. www.science.org/content/arti...
August 30, 2024 at 11:05 AM
The Lord’s work. Congrats to Emma Hodcroft and all involved. May Pathoplexus quickly supplant GISAID. www.science.org/content/arti...
👉 Make sure to register for this webinar on 27 November, in which Emma Hodcroft will present “PathoPlexus: A Community-Driven Solution for Transparent and Equitable Viral Genomic Data Sharing”.
📢 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
🎙️ 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
November 18, 2025 at 10:17 AM
👉 Make sure to register for this webinar on 27 November, in which Emma Hodcroft will present “PathoPlexus: A Community-Driven Solution for Transparent and Equitable Viral Genomic Data Sharing”.
are released to open access by other experts, who can then apply techniques they have experience in. The Pathoplexus database based in Switzerland contributes to that. Ironically, that’s remote – but not slow!
So, it’s not "just" local, but local & connected to international science infrastructure.
So, it’s not "just" local, but local & connected to international science infrastructure.
May 23, 2026 at 8:46 PM
are released to open access by other experts, who can then apply techniques they have experience in. The Pathoplexus database based in Switzerland contributes to that. Ironically, that’s remote – but not slow!
So, it’s not "just" local, but local & connected to international science infrastructure.
So, it’s not "just" local, but local & connected to international science infrastructure.