Josh Quick @scalene.bsky.social · 22/05/2026Great work by @dominikaanna.bsky.social @bede.im and the HPRU PHG team @imibirmingham.bsky.social @unibirmingham.bsky.social 010
Josh Quick @scalene.bsky.social · 22/05/2026Bottom 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. 100
Josh Quick @scalene.bsky.social · 22/05/2026We 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. 100
Josh Quick @scalene.bsky.social · 22/05/2026This 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. 100
Josh Quick @scalene.bsky.social · 22/05/2026SISPA (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. 100
Josh Quick @scalene.bsky.social · 22/05/2026New preprint from us! 🦠 Clinical metagenomics is great for sequencing pathogens directly from patient samples but for some protocols sensitivity for RNA viruses lags behind bacteria & fungi. We have shown why, and how to fix it. www.medrxiv.org/content/10.6...medrxiv.orgLibrary preparation strategy critically impacts RNA virus sensitivity in clinical metagenomicsClinical metagenomics uses sequencing for culture-independent identification of pathogens directly from clinical specimens. While a number of protocols claim to be pathogen agnostic, sensitivity for R... 11812
Reposted by Josh QuickInstitute of Microbiology and Infection @imibirmingham.bsky.social · 12/03/2026We 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... 053
Reposted by Josh QuickKristian G. Andersen @kgandersen.bsky.social · 24/02/2026New 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... 17531
Reposted by Josh QuickEd Cunningham-Oakes @edcoakes.bsky.social · 16/01/2026Love 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 Febedzz.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... 0716
Reposted by Josh QuickRick Beeloo @rickbitloo.bsky.social · 23/10/2025Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it: www.biorxiv.org/content/10.1... Want to get started? github.com/rickbeeloo/b... 35231
Josh Quick @scalene.bsky.social · 18/09/2025Excited to finally get our hands on a production Topo kit! @articnetwork.bsky.social 010
Reposted by Josh QuickBede Constantinides @bede.im · 12/08/2025Interested 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.socialartic.networkGenome assemblies for a respiratory metagenomics positive control | ARTIC network - pathogen genomics from sample to response 0114
Reposted by Josh QuickJosh Levy @josh-levy.bsky.social · 31/07/2025We’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.comgithub.comGitHub - andersen-lab/Freyja-barcodesContribute to andersen-lab/Freyja-barcodes development by creating an account on GitHub. 131
Josh Quick @scalene.bsky.social · 19/06/2025Although 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... 040
Josh Quick @scalene.bsky.social · 19/06/2025Francisella tularensis identified using @articnetwork.bsky.social SMART-9N metagenomics and @nanoporetech.com sequencing. Amazing work! 193
Josh Quick @scalene.bsky.social · 19/06/2025Click the link for open-source recipes for end-preparation, barcode and adapter ligation. 60% cost saving over commercial kits for the ARTIC protocol. 082
Reposted by Josh QuickAnna (Ganna) Kovalenko @annakovalenko.bsky.social · 15/06/2025Ever 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.combiorxiv.org 41610
Reposted by Josh QuickNick Loman @pathogenomenick.bsky.social · 22/05/2025And don't forget to watch the accompanying video of @scalene.bsky.social broodily walking the canals of Birmingham describing how sequencing can be useful in outbreaks: www.youtube.com/watch?embeds...youtube.comChanging how the world tracks emerging viruses | University of BirminghamYouTube video by University of Birmingham 0113
Josh Quick @scalene.bsky.social · 08/04/2025Job 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... 056
Reposted by Josh QuickRichard Branson @richardbranson.bsky.social · 20/02/2025President 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. 275112073120752
Reposted by Josh QuickGabrielius Landsbergis @glandsbergis.bsky.social · 15/02/2025Once 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 19159752276
Reposted by Josh QuickJohn Tyson @drt1973.bsky.social · 13/02/2025Working a treat here to, threw in some melt in nut inserts etc 😊 111
Reposted by Josh QuickWill Anderson @willaanderson.bsky.social · 12/02/2025Oh 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. 😅 131
Josh Quick @scalene.bsky.social · 13/02/2025For ONT libraries being able to measure in the range 1-100ng/ul is perfectly adequate. 110
Josh Quick @scalene.bsky.social · 13/02/2025A colleague here and I had an idea to use a dye with a larger Stokes shift which might help with some of the scatter but I honestly don’t think it’s necessary now. 100
Josh Quick @scalene.bsky.social · 13/02/2025I had been wanting to do this for a while. I got as far as dismantling one and measuring the spectra of the filter set. 310
Josh Quick @scalene.bsky.social · 13/02/2025This will be huge for LIAS because the fluorometer was one of the most expensive bits. Qubit 4 currently £2800 on our procurement system! 210
Josh Quick @scalene.bsky.social · 12/02/2025 Built our first two DIYNAFLOURS and they work great! Thanks @willaanderson.bsky.social 1120
Reposted by Josh QuickKristian G. Andersen @kgandersen.bsky.social · 05/02/2025Genotype 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. 421499
Reposted by Josh QuickUniversity of Leeds - School of Law @lawatleeds.bsky.social · 23/01/2025The @universityofleeds.bsky.social is the first Russell Group Uni to quit X! 🎉 🎉 Read more👇 tinyurl.com/2h3tyjfx @lsjleeds.bsky.social #Yorkshire #Leeds #Academia #AcademicSky #HigherEd #LawSkytinyurl.comLeeds becomes first Russell Group university to quit X - Research Professional NewsLeeds says Elon Musk’s social media site “no longer aligns with our university values” 923785
Reposted by Josh QuickLed By Donkeys @ledbydonkeys.org · 23/01/2025The world’s richest man is promoting the far right in Europe. Don’t buy a Tesla . Location: Tesla Gigafactory, Berlin www.youtube.com/watch?v=NjWl...youtube.comHeil TeslaYouTube video by Led By Donkeys 21565593045
Reposted by Josh Quick(((Tendar))) @tendar.bsky.social · 22/01/2025President 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) 21916176
Josh Quick @scalene.bsky.social · 24/12/2024Turns out it works for bacteria too, can’t believe we didn’t try that! bsky.app/profile/nath... 020
Josh Quick @scalene.bsky.social · 24/12/2024Can’t wait to see what people do with it. Merry Christmas! 031
Josh Quick @scalene.bsky.social · 24/12/2024Massive effort by @chris.primalscheme.com and @aresti.primalscheme.com check it out now at primalscheme.com 110
Josh Quick @scalene.bsky.social · 24/12/2024The latest version will perform sequence alignment and design primers can amplify whole viral species. It can also make massive schemes with thousands of primers. 210
Josh Quick @scalene.bsky.social · 24/12/2024Really 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 12510
Reposted by Josh QuickChris Kent @chris.primalscheme.com · 23/12/2024Fancy 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... 1157
Josh Quick @scalene.bsky.social · 20/12/2024If you can wait a few hours we have a preprint in the BioRxiv queue! 130
Reposted by Josh QuickChris Kent @chris.primalscheme.com · 09/12/2024primalscheme3 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 followprimalscheme.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. 1177
Josh Quick @scalene.bsky.social · 10/12/2024That’s an old advert but I’d be happy to talk to them 000
Reposted by Josh QuickPathoplexus @pathoplexus.org · 09/12/2024Today 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 28238
Josh Quick @scalene.bsky.social · 09/12/2024Thank you for doing this it's going to be incredibly useful! 194
Reposted by Josh QuickConrad Hackett @conradhackett.bsky.social · 15/11/2024Disease prevalence in US states before & after vaccine introduction Graphic from Edward Tufte More graphics.wsj.com/infectious-d... 🧪 12938721693