📋 You can find instructions for how to upload data to Pathoplexus in our docs: pathoplexus.org/docs/how-to/upload-sequences

📰 And read our full blog post on adding RSV and HMPV here: pathoplexus.org/news/2025-05-22-pathoplexus-rsv-and-hmpv

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📨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

Our Executive Board decided to prioritize adding RSV and HMPV to Pathoplexus based on feedback from the community.

This included a letter from those working on these viruses, asking that the virus be added.
Community involvement is a key part of Pathoplexus. 🤝

2/4

📢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

👀Be sure to check out the full News Item to see all our updates and information on our past and upcoming events: pathoplexus.org/news/2025-04-16-spring-update

Maybe we'll soon be at a workshop or conference near you! 😁🌍🌎

9/9

Our Executive Board has also been busy! They have had further discussions around adding new pathogens to Pathoplexus and handling finances. 📑

As part of our commitment to transparency, you can see all of our minutes online:
https://pathoplexus.org/about/governance/minutes

8/9

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

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

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

And on 21 Feb, we had 41 mpox sequences submitted from the Central African Republic, with thanks to the Institut Pasteur de Bangui, Helmholtz Institute for One Health, and Ministère de la Santé et de la Population, Bengui:

https://pathoplexus.org/mpox/search?visibility_releasedAtTimestamp=true&releasedAtTimestampFrom=1740132968&releasedAtTimestampTo=1740132970

4/9

Ebola outbreak response: On 3 Feb, the first sequence from the Ebola outbreak in Kampala, Uganda, was uploaded to Pathoplexus and described on Virological, as we reported shortly after:

https://mstdn.science/@pathoplexus/113951845136343774

2/9

We had the first Restricted-Use sequences submitted 4th Feb, with 703 mpox genomes uploaded by DRC thanks to INRB:

https://pathoplexus.org/mpox/search?visibility_groupName=true&groupName=Pathogen+Genomic+Lab

And on 7 Feb, we had an mpox sequence from INSA in Portugal uploaded the same day it was sequenced!

https://pathoplexus.org/seq/PP_0013N8P.1

3/9

🗓️ 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

Thanks to huge efforts by Uganda’s Central Public Health Laboratory, Uganda Ministry of Health, UVRI, Africa CDC & SANBI, UWC the sequence from the recent Ebola Sudan case in Kampala is now available on Pathoplexus https://pathoplexus.org/seq/PP_0011CQ4.2 with full analysis here: https://virological.org/t/near-real-time-genomic-characterization-of-the-2025-sudan-ebolavirus-outbreak-in-uganda-s-index-case-insights-into-evolutionary-origins/990

Interested in finding out more about @pathoplexus? We're running two Information/Q&A sessions!
22 Jan 15-17.00 CET
4 Feb 16-18.00 CET

Come join us & bring your questions, to find out more about using & sharing data with Pathoplexus! 😁

Sign up here: https://forms.gle/YRRZA1rRtgYyd5nw6

👀 If you'd like to check out mpox on Pathoplexus, you can head to: https://pathoplexus.org/mpox/search

📖 If you'd like to read more about adding mpox and other updates:
https://pathoplexus.org/news/2024-12-09-expanding-pathoplexus-mpox

8/7

Are you interested in learning more about how to use Pathoplexus to share mpox (or other pathogen) data?

We’d be happy to help you get started. Please let us know about your interest in taking part in an online introduction to Pathoplexus by using this form:
https://forms.gle/a5FvyWhfTbgdUigk8

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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

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

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.

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