Pathoplexus
@pathoplexus.org
An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.
pathoplexus.org
pathoplexus.org
We encourage anyone interested in using these data for publications or preprints to reach out to the authors directly. Restricted-Use sharing protects their work and encourages collaborations, while ensuring the sequences are available for public health when needed most.
7/7
7/7
September 10, 2025 at 10:00 AM
We encourage anyone interested in using these data for publications or preprints to reach out to the authors directly. Restricted-Use sharing protects their work and encourages collaborations, while ensuring the sequences are available for public health when needed most.
7/7
7/7
Restricted-Use sequences cannot be used for publications or preprints without permission from the data generators. This ensures credit and collaboration, while still supporting urgent response.
6/7
6/7
September 10, 2025 at 10:00 AM
Restricted-Use sequences cannot be used for publications or preprints without permission from the data generators. This ensures credit and collaboration, while still supporting urgent response.
6/7
6/7
Restricted-Use sequences can be used immediately for public health, outbreak response, and preparedness. This is the main purpose of this option: enabling rapid access when it matters most.
5/7
5/7
September 10, 2025 at 10:00 AM
Restricted-Use sequences can be used immediately for public health, outbreak response, and preparedness. This is the main purpose of this option: enabling rapid access when it matters most.
5/7
5/7
Since these sequences are likely to attract interest, it’s worth highlighting again what ‘Restricted-Use’ means on Pathoplexus.
Data Use Terms for Restricted-Use data: pathoplexus.org/about/terms-...
4/7
Data Use Terms for Restricted-Use data: pathoplexus.org/about/terms-...
4/7
September 10, 2025 at 10:00 AM
Since these sequences are likely to attract interest, it’s worth highlighting again what ‘Restricted-Use’ means on Pathoplexus.
Data Use Terms for Restricted-Use data: pathoplexus.org/about/terms-...
4/7
Data Use Terms for Restricted-Use data: pathoplexus.org/about/terms-...
4/7
We’re grateful these sequences were shared on Pathoplexus. The authors have chosen to share them as ‘Restricted-Use’ - enabling rapid access for public health, while limiting use in publications/preprints.
View the sequences here: pathoplexus.org/ebola-zaire/...
3/7
View the sequences here: pathoplexus.org/ebola-zaire/...
3/7
September 10, 2025 at 10:00 AM
We’re grateful these sequences were shared on Pathoplexus. The authors have chosen to share them as ‘Restricted-Use’ - enabling rapid access for public health, while limiting use in publications/preprints.
View the sequences here: pathoplexus.org/ebola-zaire/...
3/7
View the sequences here: pathoplexus.org/ebola-zaire/...
3/7
Behind these sequences are the dedicated teams leading the public health response, sampling, testing, & sequencing. With thanks to Placide Mbala-Kingebeni & team at Institute National de Recherche Biomedicale DRC @inrb_kinshasa.
See the post for a full author list.
2/7
See the post for a full author list.
2/7
September 10, 2025 at 10:00 AM
Behind these sequences are the dedicated teams leading the public health response, sampling, testing, & sequencing. With thanks to Placide Mbala-Kingebeni & team at Institute National de Recherche Biomedicale DRC @inrb_kinshasa.
See the post for a full author list.
2/7
See the post for a full author list.
2/7
We are so grateful to our contributors, curators, members & partners worldwide ❤️
Here’s to Year 2 - and an even more connected, equitable future for pathogen genomics! 🎊
Read our whole post here: pathoplexus.org/news/2025-08...
10/10
Here’s to Year 2 - and an even more connected, equitable future for pathogen genomics! 🎊
Read our whole post here: pathoplexus.org/news/2025-08...
10/10
Pathoplexus | Pathoplexus Turns One – and Adds Measles Virus!
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, 2025 at 3:57 PM
We are so grateful to our contributors, curators, members & partners worldwide ❤️
Here’s to Year 2 - and an even more connected, equitable future for pathogen genomics! 🎊
Read our whole post here: pathoplexus.org/news/2025-08...
10/10
Here’s to Year 2 - and an even more connected, equitable future for pathogen genomics! 🎊
Read our whole post here: pathoplexus.org/news/2025-08...
10/10
📢 We’re also celebrating a successful ETH4D Research Challenge grant with ETH Zurich @ethz.ch & Stephen Kanyerezi (Uganda) @kanyerezi30.bsky.social to grow Pathoplexus & Loculus – with workshops, training, user feedback & community building.
9/10
9/10
August 27, 2025 at 3:57 PM
📢 We’re also celebrating a successful ETH4D Research Challenge grant with ETH Zurich @ethz.ch & Stephen Kanyerezi (Uganda) @kanyerezi30.bsky.social to grow Pathoplexus & Loculus – with workshops, training, user feedback & community building.
9/10
9/10
💡 New tech:
🔁GISAID accessions can now be linked in metadata for supported pathogens
🖱️Drag your mouse over checkboxes to quickly select multiple sequences
🔎Find sequences faster than ever with the new Accession search at the top of the home page
8/10
🔁GISAID accessions can now be linked in metadata for supported pathogens
🖱️Drag your mouse over checkboxes to quickly select multiple sequences
🔎Find sequences faster than ever with the new Accession search at the top of the home page
8/10
August 27, 2025 at 3:57 PM
💡 New tech:
🔁GISAID accessions can now be linked in metadata for supported pathogens
🖱️Drag your mouse over checkboxes to quickly select multiple sequences
🔎Find sequences faster than ever with the new Accession search at the top of the home page
8/10
🔁GISAID accessions can now be linked in metadata for supported pathogens
🖱️Drag your mouse over checkboxes to quickly select multiple sequences
🔎Find sequences faster than ever with the new Accession search at the top of the home page
8/10
Other news:
We’ve received
🧬 256 new direct mpox sequences from Sierra Leone, Portugal, Germany, Côte d’Ivoire, DRC, Ireland & Central African Republic
🧬 308 new direct West Nile sequences from California & Nebraska, USA
7/10
We’ve received
🧬 256 new direct mpox sequences from Sierra Leone, Portugal, Germany, Côte d’Ivoire, DRC, Ireland & Central African Republic
🧬 308 new direct West Nile sequences from California & Nebraska, USA
7/10
August 27, 2025 at 3:57 PM
Other news:
We’ve received
🧬 256 new direct mpox sequences from Sierra Leone, Portugal, Germany, Côte d’Ivoire, DRC, Ireland & Central African Republic
🧬 308 new direct West Nile sequences from California & Nebraska, USA
7/10
We’ve received
🧬 256 new direct mpox sequences from Sierra Leone, Portugal, Germany, Côte d’Ivoire, DRC, Ireland & Central African Republic
🧬 308 new direct West Nile sequences from California & Nebraska, USA
7/10
Why now?
• Measles cases have surged in the US in 2025 - real-time genomic tracking is vital
• Global travel + declining vaccination rates raise outbreak risk
• More labs are sequencing MeV than ever before- enabling insights into spread & evolution
6/10
• Measles cases have surged in the US in 2025 - real-time genomic tracking is vital
• Global travel + declining vaccination rates raise outbreak risk
• More labs are sequencing MeV than ever before- enabling insights into spread & evolution
6/10
August 27, 2025 at 3:57 PM
Why now?
• Measles cases have surged in the US in 2025 - real-time genomic tracking is vital
• Global travel + declining vaccination rates raise outbreak risk
• More labs are sequencing MeV than ever before- enabling insights into spread & evolution
6/10
• Measles cases have surged in the US in 2025 - real-time genomic tracking is vital
• Global travel + declining vaccination rates raise outbreak risk
• More labs are sequencing MeV than ever before- enabling insights into spread & evolution
6/10
🎉 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
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
August 27, 2025 at 3:57 PM
🎉 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
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
And… 🏆
We received the 2024 Swiss National Open Research Data Prize for our commitment to openness & community governance – all while being powered largely by volunteer effort!
4/10
We received the 2024 Swiss National Open Research Data Prize for our commitment to openness & community governance – all while being powered largely by volunteer effort!
4/10
August 27, 2025 at 3:57 PM
And… 🏆
We received the 2024 Swiss National Open Research Data Prize for our commitment to openness & community governance – all while being powered largely by volunteer effort!
4/10
We received the 2024 Swiss National Open Research Data Prize for our commitment to openness & community governance – all while being powered largely by volunteer effort!
4/10
We’ve also:
• Enabled rapid public-health use while protecting publication rights via Restricted-Use sharing
• Presented at WHO IPSN events, major conferences & workshops
• Featured in Lancet Microbe, Science, Nature, and national media
3/10
• Enabled rapid public-health use while protecting publication rights via Restricted-Use sharing
• Presented at WHO IPSN events, major conferences & workshops
• Featured in Lancet Microbe, Science, Nature, and national media
3/10
August 27, 2025 at 3:57 PM
We’ve also:
• Enabled rapid public-health use while protecting publication rights via Restricted-Use sharing
• Presented at WHO IPSN events, major conferences & workshops
• Featured in Lancet Microbe, Science, Nature, and national media
3/10
• Enabled rapid public-health use while protecting publication rights via Restricted-Use sharing
• Presented at WHO IPSN events, major conferences & workshops
• Featured in Lancet Microbe, Science, Nature, and national media
3/10
A Year of Milestones 🌍
Together with our community we have:
• Added mpox (Dec 2024) + RSV & HMPV (May 2025)
• Received direct uploads from 5 continents - incl. more mpox in 2025 than other databases
• Rolled out major software updates & new analysis integrations
2/10
Together with our community we have:
• Added mpox (Dec 2024) + RSV & HMPV (May 2025)
• Received direct uploads from 5 continents - incl. more mpox in 2025 than other databases
• Rolled out major software updates & new analysis integrations
2/10
August 27, 2025 at 3:57 PM
A Year of Milestones 🌍
Together with our community we have:
• Added mpox (Dec 2024) + RSV & HMPV (May 2025)
• Received direct uploads from 5 continents - incl. more mpox in 2025 than other databases
• Rolled out major software updates & new analysis integrations
2/10
Together with our community we have:
• Added mpox (Dec 2024) + RSV & HMPV (May 2025)
• Received direct uploads from 5 continents - incl. more mpox in 2025 than other databases
• Rolled out major software updates & new analysis integrations
2/10
👀Be sure to check out the full News Item to see all our technical updates (we couldn’t fit them all here), new sequences, and extra information!:
pathoplexus.org/news/2025-07-14-july-update
We can’t wait to celebrate one year with you all in August! 😁🎂
9/9
pathoplexus.org/news/2025-07-14-july-update
We can’t wait to celebrate one year with you all in August! 😁🎂
9/9
Pathoplexus | Pathoplexus July 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
July 15, 2025 at 10:13 AM
👀Be sure to check out the full News Item to see all our technical updates (we couldn’t fit them all here), new sequences, and extra information!:
pathoplexus.org/news/2025-07-14-july-update
We can’t wait to celebrate one year with you all in August! 😁🎂
9/9
pathoplexus.org/news/2025-07-14-july-update
We can’t wait to celebrate one year with you all in August! 😁🎂
9/9
As you may have already seen, ARTIC2, follow-up to the hugely successful ARTIC, has launched, and through @firefoxx66.bsky.social & @swisstph.ch, Loculus (the software underlying Pathoplexus) is part of the effort to make sequencing & data sharing easier!
bsky.app/profile/path...
8/9
bsky.app/profile/path...
8/9
Absolutely thrilled to announce the launch of ARTIC2 - a £5.5M 5 year project funded by @wellcometrust.bsky.social to build on the ARTIC approach of low-cost, globally accessible genome sequencing for surveillance of outbreaks, epidemics and endemic diseases: www.birmingham.ac.uk/news/2025/am...
Ambitious project to develop low-cost genome sequencing for pathogens known and unknown - University of Birmingham
Project will build on research that helped diagnostic labs to adopt sequencing capacity for COVID-19 and permit characterisation of future infectious threats
www.birmingham.ac.uk
July 15, 2025 at 10:13 AM
As you may have already seen, ARTIC2, follow-up to the hugely successful ARTIC, has launched, and through @firefoxx66.bsky.social & @swisstph.ch, Loculus (the software underlying Pathoplexus) is part of the effort to make sequencing & data sharing easier!
bsky.app/profile/path...
8/9
bsky.app/profile/path...
8/9
We’ve also made donating to Pathoplexus easier - our new Funding page has helpful information - we will add additional donation methods soon! And we’d be happy to discuss institutional support as well - just reach out! 💶
pathoplexus.org/about/funding
7/9
pathoplexus.org/about/funding
7/9
Pathoplexus | Funding
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
July 15, 2025 at 10:13 AM
We’ve also made donating to Pathoplexus easier - our new Funding page has helpful information - we will add additional donation methods soon! And we’d be happy to discuss institutional support as well - just reach out! 💶
pathoplexus.org/about/funding
7/9
pathoplexus.org/about/funding
7/9
If you’re an API user, you’ll be happy to hear we now support advanced queries including logical queries (like ‘and’, ‘not’, ‘&’, etc), regex, and ‘N-of’ & ‘exactly-of’ for more exact & flexible matching. 🧑🏻💻
See our full docs on using them here:
lapis.cov-spectrum.org/open/v2/docs...
6/9
See our full docs on using them here:
lapis.cov-spectrum.org/open/v2/docs...
6/9
Advanced query
Generalized advanced queries
lapis.cov-spectrum.org
July 15, 2025 at 10:13 AM
If you’re an API user, you’ll be happy to hear we now support advanced queries including logical queries (like ‘and’, ‘not’, ‘&’, etc), regex, and ‘N-of’ & ‘exactly-of’ for more exact & flexible matching. 🧑🏻💻
See our full docs on using them here:
lapis.cov-spectrum.org/open/v2/docs...
6/9
See our full docs on using them here:
lapis.cov-spectrum.org/open/v2/docs...
6/9
In an awesome new feature, you can now use the ‘Tools’ button to send sequences from Pathoplexus to other analyses and visualizations - like maps or Nextclade!
Have a tool that would be worth including? See our docs!
pathoplexus.org/docs/how-to/...
5/9
Have a tool that would be worth including? See our docs!
pathoplexus.org/docs/how-to/...
5/9
July 15, 2025 at 10:13 AM
In an awesome new feature, you can now use the ‘Tools’ button to send sequences from Pathoplexus to other analyses and visualizations - like maps or Nextclade!
Have a tool that would be worth including? See our docs!
pathoplexus.org/docs/how-to/...
5/9
Have a tool that would be worth including? See our docs!
pathoplexus.org/docs/how-to/...
5/9
In new features - We’ve made it easy to include sublineages in your search! Use the ‘include sublineages’ checkbox on the website, or ‘A.2.*’ in the API to return both the top-level lineage and all sublineages:
4/9
4/9
July 15, 2025 at 10:13 AM
In new features - We’ve made it easy to include sublineages in your search! Use the ‘include sublineages’ checkbox on the website, or ‘A.2.*’ in the API to return both the top-level lineage and all sublineages:
4/9
4/9
Direct uploads in May & June have included the following sequences:
- 128 Mpox
- 15 West Nile
- 1089 RSV-A
- 1060 RSV-B
- 1 Ebola Zaire
An incredible diversity both in sequences and in contributing labs. We thank these contributors for choosing to share with Pathoplexus! 🙏🏻
3/9
- 128 Mpox
- 15 West Nile
- 1089 RSV-A
- 1060 RSV-B
- 1 Ebola Zaire
An incredible diversity both in sequences and in contributing labs. We thank these contributors for choosing to share with Pathoplexus! 🙏🏻
3/9
July 15, 2025 at 10:13 AM
Direct uploads in May & June have included the following sequences:
- 128 Mpox
- 15 West Nile
- 1089 RSV-A
- 1060 RSV-B
- 1 Ebola Zaire
An incredible diversity both in sequences and in contributing labs. We thank these contributors for choosing to share with Pathoplexus! 🙏🏻
3/9
- 128 Mpox
- 15 West Nile
- 1089 RSV-A
- 1060 RSV-B
- 1 Ebola Zaire
An incredible diversity both in sequences and in contributing labs. We thank these contributors for choosing to share with Pathoplexus! 🙏🏻
3/9