Chris Kent
@chris.primalscheme.com
π€ 339
π₯ 156
π 4
PhD student in the Quick Lab with
@articnetwork.bsky.social
reposted by
Chris Kent
Kristian G. Andersen
15 days ago
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...
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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...
https://www.medrxiv.org/content/10.64898/2026.02.21.26346782v1
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reposted by
Chris Kent
Pathoplexus
7 months ago
π 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
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reposted by
Chris Kent
Bede Constantinides
7 months ago
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
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Genome assemblies for a respiratory metagenomics positive control | ARTIC network - pathogen genomics from sample to response
https://artic.network/2025-07-26_positive-control-genome-assemblies.html
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reposted by
Chris Kent
Josh Levy
7 months ago
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). π§΅ Β
doi.org/10.1101/2025...
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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...
https://doi.org/10.1101/2025.07.26.25332245
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need an (artic)help-ing hand with enzyme availability for amplicon sequencing? 𧬠check out this new preprint from
@annakovalenko.bsky.social
featuring a new norovirus-gii scheme!
doi.org/10.1101/2025...
add a skeleton here at some point
9 months ago
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reposted by
Chris Kent
Bede Constantinides
9 months ago
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
add a skeleton here at some point
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reposted by
Chris Kent
Nick Loman
10 months ago
Absolutely thrilled to announce the launch of ARTIC2 - a Β£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...
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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
https://www.birmingham.ac.uk/news/2025/ambitious-project-to-develop-low-cost-genome-sequencing-for-pathogens-known-and-unknown
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reposted by
Chris Kent
Josh Quick
11 months ago
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...
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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...
https://edzz.fa.em3.oraclecloud.com/hcmUI/CandidateExperience/en/sites/CX_6001/job/6833/?utm_medium=jobshare&utm_source=External+Job+Share
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reposted by
Chris Kent
Andrew Rambaut (ππ)
about 1 year ago
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.
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Near Real-Time Genomic Characterization of the 2025 Sudan Ebolavirus Outbreak in Ugandaβs 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...
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
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reposted by
Chris Kent
Andrew Page
about 1 year ago
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
add a skeleton here at some point
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Fancy some light Christmas reading? Iβm happy to share our new preprint, covering the impact and cutting edge improvements to PrimalScheme! Preprint:
www.biorxiv.org/content/10.1...
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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...
https://www.biorxiv.org/content/10.1101/2024.12.20.629611v1
about 1 year ago
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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
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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.
https://primalscheme.com/
over 1 year ago
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reposted by
Chris Kent
ARTIC Network
over 1 year ago
ARTIC have primers for
#Marburg
virus! (MVD)
labs.primalscheme.com/detail/artic...
#molecularepidemiology
#pathogen
#pathogensurviellance
#bioinformatics
#epidemiology
#virus
#outbreak
#clinicalvirology
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https://labs.primalscheme.com/detail/artic-marv/1200/v1.0.0/?q=
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Very excited to be using the soon-to-be released MK1D for HBV sequencing from Uganda!
almost 2 years ago
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