Pathoplexus

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.

👀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

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...

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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.

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

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

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

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

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

Graph showing 6 months of Mpox sequences added to Pathoplexus, from Feb 2025 - July 2025, as a bar-chart. Bars are split into blue (sequences ingested from NCBI) and orange (sequences uploaded directly to Pathoplexus). The totals are approximately: - Feb: 75 from NCBI, 725 direct - Mar: 50 NCBI, ~5 direct - Apr: 75 NCBI, 225 direct - May: 100 NCBI, 100 direct - June: 50 NCBI, 75 direct - July: too small to see clearly

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

Screenshot of the July Update News article on the Pathoplexus website

🗓️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

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Pathoplexus | Mpox Virus - Browse 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.

Hi Mike! We use Nextclade for lineage calling in Pathoplexus, so you shouldn't need to run it through again.

We're also honored to have had many direct uploads from Sierra Leone now: pathoplexus.org/mpox/search?...

I hope that helps!
(Emma)

Pathoplexus | Uploading sequences 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.

📋 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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A diagram showing how users can easily upload data to Pathoplexus and choose to share this as 'Open data' which can be used by other without restriction, or 'Restricted-use' data which requires permission to publish or preprint on. Restricted-use data can be restricted for up to 1 year, after which it becomes Open, and is always available to view. Open data is automatically submitted to INDSC (Genbank, ENA, DDBJ) by Pathoplexus on behalf of the submitter.

📨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

Screenshot of the homepage of Pathoplexus, showing tiles to navigate to the supported pathogens CCHF, Ebola Sudan, Ebola Zaire, HMPV, Mpox, RSV-A, RSV-B, and West Nile virus.

📢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

two thousand code-commits to loculus, the code that powers @pathoplexus.org. teamwork/dreamwork

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.

👀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

Pathoplexus | Meeting Minutes 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.

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:
pathoplexus.org/about/govern...

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

A screenshot of the pathoplexus website, showing a form where you can upload a single sequence by filling in the fields.

A screenshot of the Pathoplexus website, highlighting the "create github issue" button at the bottom of a sequence information page.

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

Pathoplexus | Mpox Virus - Browse 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.

And on 21 Feb, we had 41 mpox sequences submitted from the Central African Republic, with thanks to the Institut Pasteur de Bangui, @helmholtz-hioh.bsky.social , and Ministère de la Santé et de la Population, Bengui:

pathoplexus.org/mpox/search?...

4/9

Pathoplexus | Mpox Virus - Browse 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.

We had the 1st Restricted-Use sequences submitted 4 Feb, with 703 mpox genomes uploaded by DRC thx to @labgenpath.bsky.social:

pathoplexus.org/mpox/search?...

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

pathoplexus.org/seq/PP_0013N...

3/9

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:

bsky.app/profile/path...

2/9

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 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

Screenshot of the virological post on the Ebolavirus sequence

Screenshot of the sequence on pathoplexus

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-...

Pathoplexus Online Introduction and Q&A Thank you for your interest in Pathoplexus! Are you interested in using Pathoplexus to upload your own sequences, either as Open or Restricted-Use? Do you have questions about how submission works, ...

Interested in finding out more about @pathoplexus.org? 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: forms.gle/YRRZA1rRtgYy...

Pathoplexus | Expanding Pathoplexus: mpox added 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.

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

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

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Pathoplexus Introduction (online) Are you interested in using Pathoplexus to upload your own sequences, either as Open or Restricted-Use? Do you have questions about how submission works, the Data Use Terms, or how we pass Open sequen...

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:
forms.gle/a5FvyWhfTbgd...

7/7

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.

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