1/ 🛠️ Our July update is here - and it's a technical one! New features for citations, search, submission, and more. Here's what's new in #Pathoplexus 👇 🔗 Full post: pathoplexus.org/news/2026-07...
Chris Kent
@chris.primalscheme.com
PhD student in the Quick Lab with @articnetwork.bsky.social
The ARTIC Primer Foundry is now live and will soon begin shipping BDBV primers on request primalscheme.com/orders
PrimalScheme: primer panels for multiplex PCR
PrimalScheme is a tool for designing primer panels for multiplex PCR. It uses a greedy algorithm to find primers for tiling amplicon generation for multiple reference genomes.
primalscheme.com
Rapid release of multiplex PCR amplicon scheme for Andes hantavirus whole genome sequencing validated on control material: www.biorxiv.org/content/10.6... @scalene.bsky.social @stevepullan.bsky.social @ukhsa.bsky.social output from HPRU in Public Health Genomics
biorxiv.org
ARTIC are hiring! Postdoctoral opportunity in metagenomics at the University of Birmingham edzz.fa.em3.oraclecloud.com/hcmUI/Candid...
Research Fellow (Postdoctoral) - School of Biosciences - 107071 - Grade 7
This post-doctoral position will contribute to both complementary programmes, developing ‘broadband’ metagenomic sequencing capabilities for rapid detection and characterisation of emerging and unknow...
edzz.fa.em3.oraclecloud.com
New preprint from our Gates-funded Modjadji initiative showing that whole-genome surveillance of measles virus from wastewater greatly expands our ability for monitoring and control. Here, with our colleagues in South Africa - U.S., unfortunately, likely up next. www.medrxiv.org/content/10.6...
Integrating measles wastewater and clinical whole-genome sequencing enables high-resolution tracking of virus evolution and transmission
Measles outbreaks have surged globally in recent years, but current surveillance systems have limited capacity to monitor measles virus (MeV) transmission and evolution at population scale. Although M...
medrxiv.org
🎉 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
Interested in respiratory metagenomics? We assembled nearly all of the virus genomes in a respiratory verification panel manufactured by ZeptoMetrix. Blog: artic.network/2025-07-26_p... Assemblies: github.com/bede/zmrp @scalene.bsky.social @pathogenomenick.bsky.social @articnetwork.bsky.social
Genome assemblies for a respiratory metagenomics positive control | ARTIC network - pathogen genomics from sample to response
artic.network
A few days ago we preprinted our Freyja 2 paper, describing the expansion of our original Freyja method to a real-time, multi-pathogen surveillance tool to track pathogen lineage prevalence and dynamics from sequencing of wastewater and other complex samples (like milk). 🧵 doi.org/10.1101/2025...
Real-time, multi-pathogen wastewater genomic surveillance with Freyja 2
Case-based infectious disease surveillance is fundamental to public health, but is resource-intensive, logistically complex, and prone to sampling bias. Wastewater testing and sequencing have increasi...
doi.org
need an (artic)help-ing hand with enzyme availability for amplicon sequencing? 🧬 check out this new preprint from @annakovalenko.bsky.social featuring a new norovirus-gii scheme! doi.org/10.1101/2025...
Reducing Supply Chain Dependencies for Viral Genomic Surveillance: Get by with a Little HELP from Commercial Enzymes already in your Lab Freezer
The COVID-19 pandemic exposed vulnerabilities in global laboratory supply chains, disrupting genomic surveillance efforts essential to epidemic response. To address this challenge, we developed ARTIC ...
doi.org
Anna (Ganna) Kovalenko@annakovalenko.bsky.social · last yr.Ever had to pause genomic surveillance due to enzyme shortages?🫣 Happy to share our new preprint with the solution inside 🦹♀️💪 biorxiv.org/content/10.110… @scalene.bsky.social @chris.primalscheme.com @pathogenomenick.bsky.social @articnetwork.bsky.social @nanoporetech.com
New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search. github.com/bede/deacon
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · last yr.Deacon: fast sequence filtering and contaminant depletion https://www.biorxiv.org/content/10.1101/2025.06.09.658732v1
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
birmingham.ac.uk
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...
Research Associate (Genomics) - School of Biosciences - 105316 - Grade 6
The successful candidate will play a crucial role in developing an innovative TB diagnostic approach, collaborating across a multidisciplinary team to advance our novel enzymatic lysis technology. Key...
edzz.fa.em3.oraclecloud.com
First genome sequence from the Ugandan Ebolavirus outbreak with analysis: virological.org/t/990 and first filovirus genome submitted to Pathoplexus database: pathoplexus.org/seq/PP_0011C.... Great (and rapid) work from the National Health Laboratory, UVRI and partners.
Near Real-Time Genomic Characterization of the 2025 Sudan Ebolavirus Outbreak in Uganda’s Index Case: Insights into Evolutionary Origins
Introduction Case History: On January 30, 2025, the Ministry of Health declared an outbreak of Sudan Ebola Virus (SUDV) Disease in Kampala, Uganda, following the death of a healthcare worker at Mula...
virological.org
I'm putting together a Microbial Bioinformatics starter pack to help get everyone connected in our community. Let me know if there are any bluesky users to be added and share so that twitter refugees can tune back in to the fantastic world microbes go.bsky.app/3ezLo7e
Fancy some light Christmas reading? I’m happy to share our new preprint, covering the impact and cutting edge improvements to PrimalScheme! Preprint: www.biorxiv.org/content/10.1...
PrimalScheme: open-source community resources for low-cost viral genome sequencing
Viral genome sequencing using the ARTIC protocol has been a vital tool for understanding the spread of epidemics including Ebola, Zika, COVID-19 and Mpox and has seen widespread adoption due to its lo...
biorxiv.org
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
PrimalScheme3: primer panels for multiplex PCR
primalscheme is a tool for designing primer panels for multiplex PCR. It uses a greedy algorithm to find primers for tiling amplicon generation for multiple reference genomes.
primalscheme.com
Very excited to be using the soon-to-be released MK1D for HBV sequencing from Uganda!
