Chris Kent

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...

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...

31.07.2025 19:16 — 👍 31    🔁 9    💬 1    📌 0

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...

15.06.2025 20:16 — 👍 3    🔁 2    💬 0    📌 0

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

13.06.2025 13:24 — 👍 58    🔁 40    💬 5    📌 2

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

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...

22.05.2025 10:57 — 👍 228    🔁 80    💬 7    📌 4

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...

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...

08.04.2025 10:42 — 👍 5    🔁 6    💬 0    📌 0

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...

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.

03.02.2025 16:32 — 👍 101    🔁 65    💬 3    📌 1

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

10.01.2025 09:38 — 👍 108    🔁 60    💬 27    📌 0

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...

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...

23.12.2024 10:36 — 👍 15    🔁 7    💬 1    📌 1

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.

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

09.12.2024 14:25 — 👍 17    🔁 7    💬 1    📌 0

ARTIC have primers for #Marburg virus! (MVD)

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

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

13.11.2024 16:12 — 👍 2    🔁 2    💬 0    📌 0

Laptop running MinKnow with MK1D

Very excited to be using the soon-to-be released MK1D for HBV sequencing from Uganda!

25.05.2024 09:18 — 👍 13    🔁 4    💬 2    📌 0