Pathoplexus
@pathoplexus.org
An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.
pathoplexus.org
pathoplexus.org
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’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
🎉 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
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
🗓 Pathoplexus turns ONE! 🎂🎉
In the past year we’ve grown from 4 pathogens to a truly global, community-driven platform for transparent, equitable & impactful pathogen sequence sharing.
📰 Read the full update: pathoplexus.org/news/2025-08...
1/10
In the past year we’ve grown from 4 pathogens to a truly global, community-driven platform for transparent, equitable & impactful pathogen sequence sharing.
📰 Read the full update: pathoplexus.org/news/2025-08...
1/10
August 27, 2025 at 3:57 PM
🗓 Pathoplexus turns ONE! 🎂🎉
In the past year we’ve grown from 4 pathogens to a truly global, community-driven platform for transparent, equitable & impactful pathogen sequence sharing.
📰 Read the full update: pathoplexus.org/news/2025-08...
1/10
In the past year we’ve grown from 4 pathogens to a truly global, community-driven platform for transparent, equitable & impactful pathogen sequence sharing.
📰 Read the full update: pathoplexus.org/news/2025-08...
1/10
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
We’ve been thrilled to see that May & June have brought with them a surge in direct uploads to Pathoplexus, across 5 of our supported pathogens, 5 continents, and 8 countries! 🎉🌎🌏
In fact, so far in 2025, Pathoplexus has received more direct mpox submissions than INSDC.
2/9
In fact, so far in 2025, Pathoplexus has received more direct mpox submissions than INSDC.
2/9
July 15, 2025 at 10:13 AM
We’ve been thrilled to see that May & June have brought with them a surge in direct uploads to Pathoplexus, across 5 of our supported pathogens, 5 continents, and 8 countries! 🎉🌎🌏
In fact, so far in 2025, Pathoplexus has received more direct mpox submissions than INSDC.
2/9
In fact, so far in 2025, Pathoplexus has received more direct mpox submissions than INSDC.
2/9
🗓️As we close in on 11 months of Pathoplexus, we’re pleased to announce many new direct sequence uploads and some exciting new features that expand Pathoplexus’ utility!
📰 You can see our full News Item here: pathoplexus.org/news/2025-07-14-july-update
1/9
📰 You can see our full News Item here: pathoplexus.org/news/2025-07-14-july-update
1/9
July 15, 2025 at 10:13 AM
🗓️As we close in on 11 months of Pathoplexus, we’re pleased to announce many new direct sequence uploads and some exciting new features that expand Pathoplexus’ utility!
📰 You can see our full News Item here: pathoplexus.org/news/2025-07-14-july-update
1/9
📰 You can see our full News Item here: pathoplexus.org/news/2025-07-14-july-update
1/9
📨As with other organisms, you can share data openly immediately or request that data be Restricted-Use for up to 1 year. Restricted-Use data is still openly available but is restricted in how it can be used in publications or preprints. 📖
3/4
3/4
May 22, 2025 at 4:06 PM
📨As with other organisms, you can share data openly immediately or request that data be Restricted-Use for up to 1 year. Restricted-Use data is still openly available but is restricted in how it can be used in publications or preprints. 📖
3/4
3/4
📢Today Pathoplexus announces the inclusion of 2 new viral pathogens: RSV (A & B) and HMPV.
These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.
1/4
These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.
1/4
May 22, 2025 at 4:06 PM
📢Today Pathoplexus announces the inclusion of 2 new viral pathogens: RSV (A & B) and HMPV.
These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.
1/4
These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.
1/4
You can also now more easily see what filters you’ve applied to your search, as they appear above the search results - making clearing them easier too!
7/9
7/9
April 16, 2025 at 3:47 PM
You can also now more easily see what filters you’ve applied to your search, as they appear above the search results - making clearing them easier too!
7/9
7/9
And if you just have one sequence to submit, that’s now simple too - as you can now submit individual sequences via an easy-to-use web form.
Spot a mistake? Scroll to the bottom of any sequence page and use the new "Report an Issue" button to let our curators know!
6/9
Spot a mistake? Scroll to the bottom of any sequence page and use the new "Report an Issue" button to let our curators know!
6/9
April 16, 2025 at 3:47 PM
And if you just have one sequence to submit, that’s now simple too - as you can now submit individual sequences via an easy-to-use web form.
Spot a mistake? Scroll to the bottom of any sequence page and use the new "Report an Issue" button to let our curators know!
6/9
Spot a mistake? Scroll to the bottom of any sequence page and use the new "Report an Issue" button to let our curators know!
6/9
In updates to Pathoplexus, you can now upload metadata as Excel files - making data sharing easier than ever (we have templates too!)
In the same vein, we now let you specify what columns in metadata files should be mapped to - no more worries if your column names differ!
5/9
In the same vein, we now let you specify what columns in metadata files should be mapped to - no more worries if your column names differ!
5/9
April 16, 2025 at 3:47 PM
In updates to Pathoplexus, you can now upload metadata as Excel files - making data sharing easier than ever (we have templates too!)
In the same vein, we now let you specify what columns in metadata files should be mapped to - no more worries if your column names differ!
5/9
In the same vein, we now let you specify what columns in metadata files should be mapped to - no more worries if your column names differ!
5/9
Thanks to huge efforts by Uganda’s Central Public Health Laboratory, Uganda Ministry of Health, UVRI, Africa CDC, & SANBI, UWC the sequence from the Ebola Sudan case in Kampala is now available on Pathoplexus pathoplexus.org/seq/PP_0011C... w full analysis here: virological.org/t/near-real-...
February 5, 2025 at 2:52 PM
Thanks to huge efforts by Uganda’s Central Public Health Laboratory, Uganda Ministry of Health, UVRI, Africa CDC, & SANBI, UWC the sequence from the Ebola Sudan case in Kampala is now available on Pathoplexus pathoplexus.org/seq/PP_0011C... w full analysis here: virological.org/t/near-real-...
Our search interface makes it easy to find the sequences you may be interested in, whether by clade or lineage, country, or even by specific mutation. Sequences are easy to filter & download both via the website or by API.
6/7
6/7
December 9, 2024 at 7:15 PM
Our search interface makes it easy to find the sequences you may be interested in, whether by clade or lineage, country, or even by specific mutation. Sequences are easy to filter & download both via the website or by API.
6/7
6/7
On upload, you can easily see & fix any issues with the sequences right in the browser.
All sequences uploaded automatically go through basic quality control & get lineages/clades assigned, adding information to the sequences. We hope to add more advanced QC measures soon.
5/7
All sequences uploaded automatically go through basic quality control & get lineages/clades assigned, adding information to the sequences. We hope to add more advanced QC measures soon.
5/7
December 9, 2024 at 7:15 PM
On upload, you can easily see & fix any issues with the sequences right in the browser.
All sequences uploaded automatically go through basic quality control & get lineages/clades assigned, adding information to the sequences. We hope to add more advanced QC measures soon.
5/7
All sequences uploaded automatically go through basic quality control & get lineages/clades assigned, adding information to the sequences. We hope to add more advanced QC measures soon.
5/7
As a reminder - when data is submitted openly, or when Restricted-Use data becomes open, Pathoplexus takes care of sending it automatically to INSDC-member databases, ensuring it is available on NCBI/Genbank, ENA, and DNA Data Bank of Japan.
4/7
4/7
December 9, 2024 at 7:15 PM
As a reminder - when data is submitted openly, or when Restricted-Use data becomes open, Pathoplexus takes care of sending it automatically to INSDC-member databases, ensuring it is available on NCBI/Genbank, ENA, and DNA Data Bank of Japan.
4/7
4/7
As with other organisms, you can share data openly immediately or request that data be Restricted-Use for up to 1 year. Restricted-Use data is still openly available but is restricted in how it can be used in publications or preprints.
3/7
3/7
December 9, 2024 at 7:15 PM
As with other organisms, you can share data openly immediately or request that data be Restricted-Use for up to 1 year. Restricted-Use data is still openly available but is restricted in how it can be used in publications or preprints.
3/7
3/7
Today Pathoplexus announces the inclusion of a new viral pathogen: mpox (previously known as monkeypox).
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
December 9, 2024 at 7:15 PM
Today Pathoplexus announces the inclusion of a new viral pathogen: mpox (previously known as monkeypox).
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
It's wonderful to have initiatives like this to support, recognise, and reward #OpenData work.
Congratulations to the other 3 fantastic winners, and to the whole Pathoplexus team, who couldn't all be with us last night!
2/2
Congratulations to the other 3 fantastic winners, and to the whole Pathoplexus team, who couldn't all be with us last night!
2/2
November 28, 2024 at 4:51 PM
It's wonderful to have initiatives like this to support, recognise, and reward #OpenData work.
Congratulations to the other 3 fantastic winners, and to the whole Pathoplexus team, who couldn't all be with us last night!
2/2
Congratulations to the other 3 fantastic winners, and to the whole Pathoplexus team, who couldn't all be with us last night!
2/2