Josh Quick

Josh Quick

@scalene.bsky.social

UKRI Future Leaders Fellow, University of Birmingham

2.1K followers446 following36 posts

Josh Quick
@scalene.bsky.social

Bottom line: library prep strategy fundamentally determines RNA virus sensitivity. Several widely-used clinical metagenomics protocols tagment cDNA directly — and may be missing viruses as a result. Avoid direct tagmentation of cDNA + dual-primer PCR when RNA virus sensitivity matters.

Josh Quick
@scalene.bsky.social

This model predicts any step that disrupts fragment length will destroy the enrichment. We tested it by comparing adapter introduction during cDNA synthesis vs tagmentation. The result was clear — SISPA recovered ALL 16 RNA viruses in our control panel. Tagmenting the cDNA recovered NONE.

Josh Quick
@scalene.bsky.social

We then spiked controls into real clinical backgrounds (low/medium/high host). SISPA methods won every time. And using a modified SMART-9N protocol, we showed single-primer PCR is a critical ingredient — switch to dual-primer PCR and enrichment collapses.

Josh Quick
@scalene.bsky.social

SISPA (sequence-independent single-primer amplification) has been used to enrich viral sequences since 1991 — but nobody had explained how it actually works. We propose it exploits the PS-effect: longer viral molecules amplify preferentially over shorter host cDNA fragments on the basis of size.

Josh Quick reposted

Institute of Microbiology and Infection
@imibirmingham.bsky.social

We are recruiting! Join Dr Josh Quick @scalene.bsky.social as a Postdoctoral Fellow in Metagenomics edzz.fa.em3.oraclecloud.com/hcmUI/Candid...

edzz.fa.em3.oraclecloud.comResearch Fellow (Postdoctoral) - School of Biosciences - 107071 - Grade 7This post-doctoral position will contribute to both complementary programmes, developing ‘broadband’ metagenomic sequencing capabilities for rapid detection and characterisation of emerging and unknow...

Josh Quick reposted

Kristian G. Andersen
@kgandersen.bsky.social

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...

medrxiv.orgIntegrating measles wastewater and clinical whole-genome sequencing enables high-resolution tracking of virus evolution and transmissionMeasles 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...

Josh Quick reposted

Ed Cunningham-Oakes
@edcoakes.bsky.social

Love microbes & omics? 🦠🧬 We’re hiring a Postdoc in Public Health Genomics at @unibirmingham.bsky.social Work on cutting-edge research with wonderful people! @wvschaik.bsky.social @halllab.bsky.social @pathogenomenick.bsky.social @scalene.bsky.social @alanmcn1.bsky.social 📅 Closes 4th Feb

edzz.fa.em3.oraclecloud.comResearch Fellow - Department of Microbes, Infection and Microbiomes - 105518 - Grade 7The post holder will work within the newly established NIHR Health Protection Unit for Public Health Genomics, a partnership between the University of Birmingham and the UK Health Security Agency. You...

Josh Quick reposted

Josh Levy
@josh-levy.bsky.social

Replying to @josh-levy.bsky.social

We’re continuing to expand the number of pathogens we support for Freyja (github.com/andersen-lab...), and developing corresponding low-cost and highly sensitive amplicon sequencing schemes as our Modjadji initiative (including @scalene.bsky.social ‬ and @chris.primalscheme.com

github.comGitHub - andersen-lab/Freyja-barcodesContribute to andersen-lab/Freyja-barcodes development by creating an account on GitHub.
Josh Quick
@scalene.bsky.social

Although SMART-9N was developed for RNA viruses, DNA pathogens can be detect either via transcripts or random amplification of genomic DNA. This is the basis of the viral arm of the @nanoporetech.com rapid metagenomic sequencing protocol (nanoporetech.com/document/rap...)

nanoporetech.comRapid metagenomic sequencing for surveillance of bacterial, fungal and viral pathogens using SQK-RPB114.24This protocol: - is a rapid method to perform metagenomic sequencing for identification of bacterial, fungal and viral pathogens. - consists of a two-in-one method that splits sample into bacterial/f...
Josh Quick
@scalene.bsky.social

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

Anna (Ganna) Kovalenko@annakovalenko.bsky.social

the link to the preprint 🔗 www.biorxiv.org/content/10.1...

biorxiv.orgReducing Supply Chain Dependencies for Viral Genomic Surveillance: Get by with a Little HELP from Commercial Enzymes already in your Lab FreezerThe 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 ...
Josh Quick
@scalene.bsky.social

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.comResearch Associate (Genomics) - School of Biosciences - 105316 - Grade 6The 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...

Josh Quick reposted

Richard Branson
@richardbranson.bsky.social

President Zelenskyy has been one of the greatest leaders of our time, guiding Ukraine through the darkest period of its recent history, rising up to Russia’s unwarranted aggression, being an inspiration to the Ukrainian people and ensuring that Ukraine’s voice is heard on the world stage.

Josh Quick reposted

Gabrielius Landsbergis
@glandsbergis.bsky.social

Once again I am leaving the Munich Security Conference in a low mood. Amongst all the noise, the US signalled their plans for Europe, so things are becoming clearer. But things are clearly not good. This is what we now know, and what we have to do about it:🧵1/17

Josh Quick reposted

Will Anderson
@willaanderson.bsky.social

Replying to @willaanderson.bsky.social

Oh and Josh, I just wanted to let you know that I refer to your excellent 'lab-in-a-suitcase' work as a primary example of situations where the DIYNAFLUOR may find utility. It typically shows up in the first 1 or 2 slides of any presentation I make. 😅

Josh Quick reposted

Kristian G. Andersen
@kgandersen.bsky.social

Genotype D1.1 of H5N1 confirmed in Nevada cattle, which is the one circulating in birds and not B3.13, causing the wider cattle epizootic in the U.S. In other words, this is a second observed jump from birds into cows. Keep rolling the dice, shall we? www.feedstuffs.com/agribusiness...

feedstuffs.comNew HPAI genotype found in Nevada dairy cowsAPHIS confirms first detection of D1.1 genotype in dairy cattle through NMTS testing.

Josh Quick reposted

(((Tendar)))
@tendar.bsky.social

President Trump will learn pretty soon that Putin cannot be convinced with money, at least not any more. He is the richest person in Russia already, though he will never say no to more billions, but that wasn't the point of him starting the full scale war in Ukraine. (Thread)

Josh Quick
@scalene.bsky.social

Really glad this is out there; a lot has happened in the 7 years since the original paper including: -67,000 schemes designed by the community -18M genome sequences using PrimalScheme

Chris Kent@chris.primalscheme.com

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...

biorxiv.orgPrimalScheme: open-source community resources for low-cost viral genome sequencingViral 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...
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Josh Quick
@scalene.bsky.social

Really glad this is out there; a lot has happened in the 7 years since the original paper including: -67,000 schemes designed by the community -18M genome sequences using PrimalScheme

Chris Kent@chris.primalscheme.com

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...

biorxiv.orgPrimalScheme: open-source community resources for low-cost viral genome sequencingViral 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...

Josh Quick reposted

Chris Kent
@chris.primalscheme.com

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...

biorxiv.orgPrimalScheme: open-source community resources for low-cost viral genome sequencingViral 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...

Josh Quick reposted

Chris Kent
@chris.primalscheme.com

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

primalscheme.comPrimalScheme3: primer panels for multiplex PCRprimalscheme 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.

Josh Quick reposted

Pathoplexus
@pathoplexus.org

Today Pathoplexus announces the inclusion of a new viral pathogen: mpox (previously known as monkeypox). Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response. 1/7

Josh Quick
@scalene.bsky.social

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

Will Anderson@willaanderson.bsky.social

Hey #HiSciSky 👋. I'm a post-doc researcher with a background in scientific device dev. I have just released an open-source STEM-Education project for a $40, 3D-printed, DNA fluorometer with ng/uL levels of sensitivity. Follow for updates! GitHub Repo: github.com/traulab/DIYN... #DIYNAFLUOR #STEM

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