ARTIC Network

Click the link for open-source recipes for end-preparation, barcode and adapter ligation. 60% cost saving over commercial kits for the ARTIC protocol.

Pathoplexus | SeqSets 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.

Amazing work from our colleagues in Sierra Leone, Nigeria, and elsewhere, making the first sequences available from the ongoing Mpox epidemic in Sierra Leone.

More to come - for now, head over to @pathoplexus.org:

pathoplexus.org/seqsets/PP_S...

Super exciting that we're now up to eight viruses supported on Pathoplexus - with lots of other exciting features in the pipeline too!

**NEW Doctoral Training Programme just launched!!** This exciting programme on Microbial Genomics for Health Protection is joint between @imibirmingham.bsky.social and UKHSA @ukhsa.bsky.social. 9 brilliant projects available!!

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.

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Metagenomic Methods Development for Public Health Genomics and Pandemic Preparedness at University of Birmingham on FindAPhD.com PhD Project - Metagenomic Methods Development for Public Health Genomics and Pandemic Preparedness at University of Birmingham, listed on FindAPhD.com

PhD opportunity!

www.findaphd.com/phds/project...

The Last of Us: Developing a Genomic Epidemiology Toolkit for Fungal Outbreaks at University of Birmingham on FindAPhD.com PhD Project - The Last of Us: Developing a Genomic Epidemiology Toolkit for Fungal Outbreaks at University of Birmingham, listed on FindAPhD.com

PhD opportunity!

www.findaphd.com/phds/project...

ARTIC 2 is here!

Tracking emerging viruses - University of Birmingham Our researchers are developing fast and portable virus sequencing techniques to track viruses in areas with limited medical resources.

www.birmingham.ac.uk/news/2025/tr...

Tracking emerging viruses - University of Birmingham Our researchers are developing fast and portable virus sequencing techniques to track viruses in areas with limited medical resources.

www.birmingham.ac.uk/news/2025/tr...

UK launch metagenomic pathogen surveillance programme On Jan 30, 2025, the UK Health Security Agency (UKHSA) announced the launch of the metagenomics Surveillance Collaboration and Analysis Programme (mSCAPE)—the world’s first biosecurity surveillance sy...

Thanks to @lancetmicrobe.bsky.social for featuring our mSCAPE metagenomics surveillance collaboration and also thanks for the considered comments from Mario Falchi and Judy Breuer: www.thelancet.com/journals/lan... - keep an eye out on mSCAPE.climb.ac.uk for further details and resources

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

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Job opportunity working with myself and @pmoyniha.bsky.social on an exciting Gates funded project developing TB lysis enzymes for rapid diagnostics. edzz.fa.em3.oraclecloud.com/hcmUI/Candid...

edzz.fa.em3.oraclecloud.com/hcmUI/Candid...

Earlier this month ARTIC, together with Asia PGI, were hosted by the Ministry of Public Health in Bangkok, to conduct a regional training workshop of #MPOX #genomicsurveillance, organised by the South-East Asian WHO office, with attendees from 8 countries.

In collaboration with CLIMB BIG DATA & @articnetwork.bsky.social, we are hosting the 2-day 'Cloud Computing in Africa conference under the theme: Building Sustainable Digital Infrastructure for Pathogen Genomics,' to better understand and improve population health and health care systems in #Africa.

UKHSA launches new metagenomic surveillance for health security The UK launches mSCAPE, a world-first metagenomics initiative by UKHSA to enhance health security through rapid pathogen detection and surveillance.

Our mSCAPE project has been formally announced to the world by @smhopkins.bsky.social at #FOG2025 today: www.gov.uk/government/n... - a really exciting academic-public health collaboration to build a surveillance platform leveraging NHS metagenomic diagnostic data. @meerac.bsky.social

Does your team deposit and access pathogen genomic data via data-sharing platforms for public health use? Participate in WHO's online consultation on the critical features of pathogen genomic data-sharing platforms to meet public health needs.

All info here: www.who.int/news-room/ar...

Applied Bioinformatics and Public Health Microbiology (hybrid conference) Dates: 21-23 May 2025 Location: Hinxton Hall Conference Centre, Wellcome Genome Campus, UK and online Bursary deadline: 25 February 2025 Abstract deadline: 25 March 2025 In-person registration deadline: 29 April 2025 Virtual registration deadline: 13 May 2025

Bursary support is available to attend Applied Bioinformatics and Public Health Microbiology 2025!💰 #ABPHM25

Join us to explore the impact of data-driven #genomics on global #PublicHealth 🧬

Apply by 25 February to be considered for up to 50% off the fee. #Bursaries

📎Find out more: bit.ly/4fc0T28

Fieldbioinformatics Updates > Fieldbioinformatics updated to 1.6.0 Fieldbioinformatics has been the first line recommendation by the artic network for generation of consensus sequences from Nanopore viral amplicon sequencing d...

I've written a quick post about the recent changes to the @articnetwork.bsky.social fieldbioinformatics pipeline

virological.org/t/fieldbioin...

Thank you for doing this it's going to be incredibly useful!

The official announcement:

bsky.app/profile/path...

primalscheme3 is now live at primalscheme.com!

Key features
- Handle up to 20% target diversity
- Create panels for multiple targets
- Improved multiplexing, allowing 10x more primer per reaction

Preprint to follow

International Pathogen Surveillance Network announces first recipients of grants to better understand disease threats The World Health Organization (WHO) and partners announced ten projects that will receive almost US$ 2 million in grants to improve capacities in pathogen genomic surveillance.

“Pandemics and epidemics continue to be a global threat, further amplified by climate change. There is urgent need for equitable access to these tools and capabilities to protect lives in vulnerable communities.”

www.who.int/news/item/26...

Preliminary analysis of 98 genomic sequences of MPXV clade Ib cases from Burundi, July to September 2024 Preliminary analysis of 98 genomic sequences of MPXV clade Ib cases from Burundi, July to September 2024 Introduction A large mpox clade Ib virus outbreak started in the province of South Kivu in th...

Fabulous work with colleagues in Burundi, who took up Mpox sequencing to understand the situation AND are willing to share pre-publication, shows the expanding tree, and evidence for several introductions not taking off. In progress virological.org/t/preliminar...

ARTIC have primers for #Marburg virus! (MVD)

labs.primalscheme.com/detail/artic...

#molecularepidemiology #pathogen #pathogensurviellance #bioinformatics #epidemiology #virus #outbreak #clinicalvirology

Wendy Barclay and I will soon be recruiting a postdoc to work on a virology project investigating the evolution of swine influenza viruses and how this impacts future pandemic potential.
Job will be based at Imperial's South Kensington campus. Drop me a DM/email for more details.

Protecting the public from health threats - University of Birmingham New Health Protection Research Units will help responses to future incidents including terrorism and pandemics

Delighted that Birmingham has been awarded HPRU status in Public Health Genomics! Am looking forward to working with stellar team from UKHSA and Birmingham on themes inc. env surveillance, metagenomics, novel genomics methods & analysis/data infrastructure www.birmingham.ac.uk/news/2024/pr...

Respiratory virus detection and sequencing from negative SARS-CoV-2 rapid antigen tests medRxiv - The Preprint Server for Health Sciences

This is exciting work

'Respiratory virus detection and sequencing from negative SARS-CoV-2 rapid antigen tests'

www.medrxiv.org/content/10.1...

Confused about the mpox outbreaks? Here’s what’s spreading, where, and why With three virus variants on the move in different populations, “it keeps getting more complicated by the day”

I’ve read a lot of stuff about #mpox already that is wrong or at least confused. And it’s not that surprising. The situation is pretty complicated and confusing. I tried to disentangle a few things for Science here (thread to come later):

www.science.org/content/arti...