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Jonathan Haars

@jonathanhaars.bsky.social
727 followers 1.9K following 42 posts

PhD-student in clinical microbiology at Uppsala University and Uppsala University Hospital, Sweden. Interested in Nanopore sequencing, metagenomics, SARS-CoV-2 and more.

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Reposted by Jonathan Haars
Jonathan Haars @jonathanhaars.bsky.social · 18/04/2026
Enjoying ESCMID Global 2026 in Munich. Thank you to everyone who visited my poster. If you missed it you can search for my name in the ESCMID app #ESCMIDGlobal2026
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Jonathan Haars @jonathanhaars.bsky.social · 18/04/2026
Enjoying ESCMID Global 2026 in Munich. Thank you to everyone who visited my poster. If you missed it you can search for my name in the ESCMID app #ESCMIDGlobal2026
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Reposted by Jonathan Haars
Jonathan Haars @jonathanhaars.bsky.social · 27/02/2026
My latest scientific article: pubmed.ncbi.nlm.nih.gov/41529381/ 🧪 #Science #Research #Viruses #Biology #Sequencing
pubmed.ncbi.nlm.nih.gov
Twist-ONT: Combining nanopore sequencing with the twist comprehensive viral research panel - PubMed
The Twist Comprehensive Viral Research Panel (Twist CVRP) is a probe-based hybridization capture enrichment method for whole-genome sequencing, designed to target all known pathogenic viruses. Unlike shotgun metagenomics, where human DNA dominates, this method enriches for viral sequences within sam …
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Jonathan Haars @jonathanhaars.bsky.social · 27/02/2026
My latest scientific article: pubmed.ncbi.nlm.nih.gov/41529381/ 🧪 #Science #Research #Viruses #Biology #Sequencing
pubmed.ncbi.nlm.nih.gov
Twist-ONT: Combining nanopore sequencing with the twist comprehensive viral research panel - PubMed
The Twist Comprehensive Viral Research Panel (Twist CVRP) is a probe-based hybridization capture enrichment method for whole-genome sequencing, designed to target all known pathogenic viruses. Unlike shotgun metagenomics, where human DNA dominates, this method enriches for viral sequences within sam …
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Jonathan Haars @jonathanhaars.bsky.social · 30/01/2026
I am now on Mastodon as well if you prefer that social site: mastodon.social/@Jonathan_Ha... #Mastodon #Research
mastodon.social
Jonathan Haars (@Jonathan_Haars@mastodon.social)
0 Posts, 0 Following, 0 Followers · PhD-student in clinical microbiology at Uppsala University and Uppsala University Hospital, Sweden. Interested in Nanopore sequencing, metagenomics, SARS-CoV-2 and...
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Reposted by Jonathan Haars
Jonathan Haars @jonathanhaars.bsky.social · 20/01/2026
Interested in virome sequencing on @nanoporetech.com instruments? Check out our latest paper where we publish Twist-ONT, a modified protocol for the Twist Comprehensive Viral Research Panel (by @twistbioscience.com) so that it can be used with ONT. www.sciencedirect.com/science/arti... 🧵1/7 🧪
sciencedirect.com
Twist-ONT: Combining nanopore sequencing with the twist comprehensive viral research panel
The Twist Comprehensive Viral Research Panel (Twist CVRP) is a probe-based hybridization capture enrichment method for whole-genome sequencing, design…
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Reposted by Jonathan Haars
Rasmus Kirkegaard @kirk3gaard.bsky.social · 21/03/2025
Want @nanoporetech.com data for benchmarking microbe related stuff? Check our data for pure cultures, @zymoresearch.bsky.social mocks and metagenomes ( github.com/Kirk3gaard/M...). Basecalled reads with methylation is in @enasequence.bsky.social . Eventually the pod5s might go there as well.
github.com
GitHub - Kirk3gaard/MicroBench: Overview of our data for microbial genomic benchmarking
Overview of our data for microbial genomic benchmarking - Kirk3gaard/MicroBench
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Jonathan Haars @jonathanhaars.bsky.social · 20/01/2026
Interested in virome sequencing on @nanoporetech.com instruments? Check out our latest paper where we publish Twist-ONT, a modified protocol for the Twist Comprehensive Viral Research Panel (by @twistbioscience.com) so that it can be used with ONT. www.sciencedirect.com/science/arti... 🧵1/7 🧪
sciencedirect.com
Twist-ONT: Combining nanopore sequencing with the twist comprehensive viral research panel
The Twist Comprehensive Viral Research Panel (Twist CVRP) is a probe-based hybridization capture enrichment method for whole-genome sequencing, design…
11312
Reposted by Jonathan Haars
fly paper broadcast @fly-broadcast.bsky.social · 10/12/2025
A co-speciation dilemma and a lifestyle transition with genomic consequences in Wolbachia of Neotropical Drosophila #Drosophila
pubmed.ncbi.nlm.nih.gov
A co-speciation dilemma and a lifestyle transition with genomic consequences in Wolbachia of Neotropical Drosophila #Drosophila
PubMed link
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Reposted by Jonathan Haars
Jonathan Haars @jonathanhaars.bsky.social · 11/06/2025
At the 8th Nordic Conference of Antiviral Treatments Strategies and Drug Resistance at the beautiful Norrlands Nation in Uppsala, arranged by my co-supervisor Johan Lennerstrand 🧪 #Science #Antivirals #HIV #SARSCoV2 #Hepatitis #Virology
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Jonathan Haars @jonathanhaars.bsky.social · 11/06/2025
At the 8th Nordic Conference of Antiviral Treatments Strategies and Drug Resistance at the beautiful Norrlands Nation in Uppsala, arranged by my co-supervisor Johan Lennerstrand 🧪 #Science #Antivirals #HIV #SARSCoV2 #Hepatitis #Virology
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Reposted by Jonathan Haars
Jonathan Haars @jonathanhaars.bsky.social · 09/06/2025
A summary of our recent study on SARS-CoV-2 and monoclonal antibodies was published in Physician's Weekly 🧪 www.physiciansweekly.com/mutation-pat... #COVID19 #SARSCoV2 #Science
physiciansweekly.com
Mutation Patterns Threaten Monoclonal Antibody Utility
The following is a summary of “Dynamics of SARS-CoV-2 variants and mutations in Central Sweden between 2023 and 2024 and their potential implications on monoclonal antibodies pemivibart and sipavibart...
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Jonathan Haars @jonathanhaars.bsky.social · 09/06/2025
A summary of our recent study on SARS-CoV-2 and monoclonal antibodies was published in Physician's Weekly 🧪 www.physiciansweekly.com/mutation-pat... #COVID19 #SARSCoV2 #Science
physiciansweekly.com
Mutation Patterns Threaten Monoclonal Antibody Utility
The following is a summary of “Dynamics of SARS-CoV-2 variants and mutations in Central Sweden between 2023 and 2024 and their potential implications on monoclonal antibodies pemivibart and sipavibart...
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Reposted by Jonathan Haars
Jonathan Haars @jonathanhaars.bsky.social · 16/05/2025
A Genomic Medicine Sweden project that our lab was part of has been published, 16S sequencing using #nanopore #sequencing 🧪 link.springer.com/article/10.1... #Science #Research #Microbiology
link.springer.com
Nationwide multicentre study of Nanopore long-read sequencing for 16S rRNA-species identification - European Journal of Clinical Microbiology & Infectious Diseases
Purpose Recent improvements in Nanopore sequencing chemistry has made it a promising platform for long-read 16S rRNA sequencing. This study evaluated its clinical utility in a nationwide collaboration...
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Reposted by Jonathan Haars
Jonathan Haars @jonathanhaars.bsky.social · 31/05/2025
Comprehensive transcriptome assessment in PBMCs of post-COVID patients at a median follow-up of 28 months after a mild COVID infection reveals upregulation of JAK/STAT signaling and a prolonged immune response 🧪 #COVID19 #SARSCoV2 #PostCovid #LongCovid #PASC doi.org/10.3389/fimm...
doi.org
Frontiers | Comprehensive transcriptome assessment in PBMCs of post-COVID patients at a median follow-up of 28 months after a mild COVID infection reveals upregulation of JAK/STAT signaling and a prol...
BackgroundPost-acute sequelae of SARS-CoV-2 infection (PASC), also known as post-COVID-19 condition (here abbreviated as post-COVID) is an escalating global ...
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Reposted by Jonathan Haars
Jonathan Haars @jonathanhaars.bsky.social · 29/05/2025
Happy to share our latest scientific article, “Dynamics of SARS-CoV-2 variants and mutations in Central Sweden between 2023 and 2024 and their potential implications on monoclonal antibodies pemivibart and sipavibart as PrEP in the region” #COVID19 #SARSCoV2 www.tandfonline.com/doi/full/10.... 🧵1 🧪
tandfonline.com
Dynamics of SARS-CoV-2 variants and mutations in Central Sweden between 2023 and 2024 and their potential implications on monoclonal antibodies pemivibart and sipavibart as PrEP in the region
Monoclonal antibodies (mAbs) are an important option against SARS-CoV-2, especially as pre-exposure prophylaxis (PrEP) for patients with immune system impairment. PrEP mAbs like sipavibart and pemi...
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Jonathan Haars @jonathanhaars.bsky.social · 31/05/2025
Comprehensive transcriptome assessment in PBMCs of post-COVID patients at a median follow-up of 28 months after a mild COVID infection reveals upregulation of JAK/STAT signaling and a prolonged immune response 🧪 #COVID19 #SARSCoV2 #PostCovid #LongCovid #PASC doi.org/10.3389/fimm...
doi.org
Frontiers | Comprehensive transcriptome assessment in PBMCs of post-COVID patients at a median follow-up of 28 months after a mild COVID infection reveals upregulation of JAK/STAT signaling and a prol...
BackgroundPost-acute sequelae of SARS-CoV-2 infection (PASC), also known as post-COVID-19 condition (here abbreviated as post-COVID) is an escalating global ...
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Jonathan Haars @jonathanhaars.bsky.social · 29/05/2025
Happy to share our latest scientific article, “Dynamics of SARS-CoV-2 variants and mutations in Central Sweden between 2023 and 2024 and their potential implications on monoclonal antibodies pemivibart and sipavibart as PrEP in the region” #COVID19 #SARSCoV2 www.tandfonline.com/doi/full/10.... 🧵1 🧪
tandfonline.com
Dynamics of SARS-CoV-2 variants and mutations in Central Sweden between 2023 and 2024 and their potential implications on monoclonal antibodies pemivibart and sipavibart as PrEP in the region
Monoclonal antibodies (mAbs) are an important option against SARS-CoV-2, especially as pre-exposure prophylaxis (PrEP) for patients with immune system impairment. PrEP mAbs like sipavibart and pemi...
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Reposted by Jonathan Haars
Ryan Hisner @ryanhisner.bsky.social · 02/05/2025
Incredible how quickly Yunlong Cao & co provide us w/info on the latest emerging SARS-CoV-2 variants. Already, we have great data on BA.3.2 (the divergent saltation lineage detected in South Africa & the Netherlands & NB.1.8.1, an emerging contender for global dominance. 1/9
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Reposted by Jonathan Haars
Raj Rajnarayanan @rajlabn.bsky.social · 19/05/2025
Tracking #SARSCoV2 lineage NB.1.8.1 - Globally 4/n
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Jonathan Haars @jonathanhaars.bsky.social · 16/05/2025
A Genomic Medicine Sweden project that our lab was part of has been published, 16S sequencing using #nanopore #sequencing 🧪 link.springer.com/article/10.1... #Science #Research #Microbiology
link.springer.com
Nationwide multicentre study of Nanopore long-read sequencing for 16S rRNA-species identification - European Journal of Clinical Microbiology & Infectious Diseases
Purpose Recent improvements in Nanopore sequencing chemistry has made it a promising platform for long-read 16S rRNA sequencing. This study evaluated its clinical utility in a nationwide collaboration...
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Jonathan Haars @jonathanhaars.bsky.social · 24/04/2025
www.researchsquare.com/article/rs-5... 🧪
researchsquare.com
The Effect of Absent or Deferred Antibiotic Treatment on Pharyngotonsillitis Complications in Primary Care Before, During, and After the COVID-19 pandemic
This study explored trends in antibiotic use and the risk of complications for pharyngotonsillitis in Swedish primary care before, during and after the pandemic. Using register-based data from 295,972...
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Jonathan Haars @jonathanhaars.bsky.social · 24/04/2025
www.microbiologyresearch.org/content/jour... 🧪
microbiologyresearch.org
Evaluation of nationwide analysis surveillance for methicillin-resistant Staphylococcus aureus within Genomic Medicine Sweden
Background. National epidemiological investigations of microbial infections greatly benefit from the increased information gained by whole-genome sequencing (WGS) in combination with standardized appr...
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Reposted by Jonathan Haars
Eric Topol @erictopol.bsky.social · 25/02/2025
Peto's Paradox—that cancer does not increase with body size of mammals—was wrong. A new, comprehensive study of 263 species documents higher cancer prevalence with increasing body mass. Some large animals (e.g. elephants) have some built-in genetic adaptations www.pnas.org/doi/10.1073/... @pnas.org
pnas.org
No evidence for Peto’s paradox in terrestrial vertebrates | PNAS
Larger, longer-lived species are expected to have a higher cancer prevalence compared to smaller, shorter-lived species owing to the greater number...
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Reposted by Jonathan Haars
Adela Alcolea-Medina @adelaam.bsky.social · 04/02/2025
This is the updated metagenomics protocol for respiratory samples search.app/V491AEp3tmB7...
search.app
Pan-microbial metagenomics protocol v1.2Public workspaceCritical
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Jonathan Haars @jonathanhaars.bsky.social · 23/01/2025
New #preprint from our #research group, Campylobacter jejuni isolated from wild birds and free-range poultry were whole-genome sequenced: papers.ssrn.com/sol3/papers.... #WGS #Science #Bacteria 🧪
papers.ssrn.com
Whole Genome Sequencing of Clinically Relevant Campylobacter Jejuni Isolated from Wild Birds and Free-Range Poultry in Bangladesh
Campylobacter jejuni is a zoonotic pathogen causing potential hazards for both humans and animals. Wild birds and domesticated poultry species may be potential
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Reposted by Jonathan Haars
Love Dalén @lovedalen.bsky.social · 07/01/2025
At Stockholm University, we are now starting a 2-year Master’s programme in Evolutionary Genomics! Topics include population genetics, phylogenetics, molecular & genome evolution, DNA sequencing, bioinformatics, and palaeogenetics. Please spread the word! www.su.se/english/sear...
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Erik Karlsson @eakarlsson.bsky.social · 20/12/2024
Tis the season for #holiday lights. #avianinfluenza sequencing up and running on our new #mk1d from ⁦‪Oxford Nanopore at ⁦‪Pasteur Cambodia‬⁩ . #nanopore #oxfordnanopre #genomic #h5n1 #alliwantforchristmas #anywhereanything #virosky #idsky 🧪🦠🧬🔬🥼🥼🧑‍🔬
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Reposted by Jonathan Haars
Laurits Skov @lauritsskov.bsky.social · 02/12/2024
Very excited (and a bit nervous) to announce that I will be hiring two Postdocs for my new group(!) in Copenhagen to study the Neanderthal and Denisovan DNA which survives in present-day humans. Retweet will be much appreciated :) Link for application: candidate.hr-manager.net/ApplicationI...
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Jonathan Haars @jonathanhaars.bsky.social · 10/12/2024
Been a while since I used adaptive sampling, and first time since some new upgrades were listed in the MinKnow update notes. Looking forward to analysing the results. 🧪 #Nanopore #Sequencing #Microbiology
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Reposted by Jonathan Haars
Jonathan Haars @jonathanhaars.bsky.social · 05/12/2024
One reason why we could sequence so many SARS-CoV-2 samples at the height of testing was because of very easy to use tools and workflows for analysis. When the person doing routine work in the lab can start everything without the need for a specialist everything speeds up doi.org/10.3390/ijms... 🧪
doi.org
From SARS-CoV-2 to Global Preparedness: A Graphical Interface for Standardised High-Throughput Bioinformatics Analysis in Pandemic Scenarios and Surveillance of Drug Resistance
The COVID-19 pandemic highlighted the need for a rapid, convenient, and scalable diagnostic method for detecting a novel pathogen amidst a global pandemic. While command-line interface tools offer aut...
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Reposted by Jonathan Haars
Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 04/12/2024
In 2015 we discovered 'Loki', the first member of the Asgard archaea, the closest relatives of eukaryotes. Did you know that in stead of Lokiarchaea, we considered the name Eoarchaea. 'Eo' after Eos, the greek goddess of dawn, and in reference to the eocyte hypothesis for the origin of eukaryotes.
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Jonathan Haars @jonathanhaars.bsky.social · 05/12/2024
One reason why we could sequence so many SARS-CoV-2 samples at the height of testing was because of very easy to use tools and workflows for analysis. When the person doing routine work in the lab can start everything without the need for a specialist everything speeds up doi.org/10.3390/ijms... 🧪
doi.org
From SARS-CoV-2 to Global Preparedness: A Graphical Interface for Standardised High-Throughput Bioinformatics Analysis in Pandemic Scenarios and Surveillance of Drug Resistance
The COVID-19 pandemic highlighted the need for a rapid, convenient, and scalable diagnostic method for detecting a novel pathogen amidst a global pandemic. While command-line interface tools offer aut...
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Reposted by Jonathan Haars
Flo Débarre @flodebarre.eurosky.social · 04/12/2024
Ecology-Evolution scientific societies on Bluesky: ESEB: @eseb.bsky.social SSE: @sse-evolution.bsky.social ASN: @asn-amnat.bsky.social SMBE: @official-smbe.bsky.social BES: @britishecolsoc.bsky.social CSEE-SCEE: @csee-scee.bsky.social and joining us today, welcome!: SFE2: @sfecologie.bsky.social
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Jonathan Haars @jonathanhaars.bsky.social · 03/12/2024
The research group I'm part of is hosting the Genomic Medicine Sweden Infectious Diseases Meeting in Uppsala. Two fun and interesting days.🧪
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Jonathan Haars @jonathanhaars.bsky.social · 15/10/2024
Used DALL-E through #ChatGPT to generate a very specific clipart for a presentation in a course I'm taking. Just needed a few small manual edits in paint. net and then it was ready. Very handy. #AIart
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Jonathan Haars @jonathanhaars.bsky.social · 09/10/2024
My first article was published last year. Showed our #SARS-CoV-2 whole-genome #sequencing results from the Uppsala & Örebro regions of Sweden for 2022-2023. Mutation tracking during this period was interesting and affected monoclonal antibodies used to treat patients. www.mdpi.com/2076-2607/11...
mdpi.com
Prevalence of SARS-CoV-2 Omicron Sublineages and Spike Protein Mutations Conferring Resistance against Monoclonal Antibodies in a Swedish Cohort during 2022–2023
Monoclonal antibodies (mAbs) are an important treatment option for COVID-19 caused by SARS-CoV-2, especially in immunosuppressed patients. However, this treatment option can become ineffective due to ...
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Jonathan Haars @jonathanhaars.bsky.social · 08/10/2024
Hi everyone on BlueSky! I'm Jonathan Haars, a PhD-student at Uppsala University and Uppsala University Hospital. I have a background in evolutionary #Biology but now my focus is on #Microbiology, #Virology and #Metagenomics. I work a lot with PCR and #Nanopore sequencing, #SciComm #Science
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Jonathan Haars @jonathanhaars.bsky.social · 23/09/2024
Dropping my entire Zotero library into VOSviewer turns out to be a fun way of showing my science interests and how various research topics and previous student projects are connected.
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