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Jonathan Haars

@jonathanhaars.bsky.social
728 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
Demultiplexed raw data is available at SRA and SARS-CoV-2 and Influenza A sequences are available at GenBank. 🧵7/7
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Jonathan Haars @jonathanhaars.bsky.social · 20/01/2026
A step-by-step protocol is available at protocols.io: DOI: dx.doi.org/10.17504/protocols.io.36wgqn825gk5/v1 🧵6/7
protocols.io
Bring structure to your research - protocols.io
A secure platform for developing and sharing reproducible methods.
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Jonathan Haars @jonathanhaars.bsky.social · 20/01/2026
Next we are going to use this protocol to study other research questions, such as cancer cell viromes as well as #SARS-CoV-2 co-infections with other viruses. 🧵5/7
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Jonathan Haars @jonathanhaars.bsky.social · 20/01/2026
We managed to get several high coverage sequences of #SARS-CoV-2 and #Influenza A from previously frozen clinical nasopharyngeal and throat swab samples. We also detected a variety of other #viruses in these samples as well as plasma samples. 🧵4/7
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Jonathan Haars @jonathanhaars.bsky.social · 20/01/2026
However, no #Nanopore protocol was available for Twist CVRP. So we decided to try and adapt the existing protocols and create a new protocol, Twist-ONT, for combining Twist with Nanopore sequencing. And we were able to make it work! 🧵3/7
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Jonathan Haars @jonathanhaars.bsky.social · 20/01/2026
The Twist Comprehensive Viral Research Panel (CVRP) is able to enrich viral pathogens through a design based on over 15,000 strains, which covers all known pathogenic viruses. We wanted to use this powerful technique with our Oxford Nanopore GridION instrument. 🧵2/7 #Virology #Metagenomics #Science
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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
Link to the original research article: www.tandfonline.com/doi/full/10.... 🧪
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 · 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
Karin Elfving, Anna-Karin Jonsson and Hong Yin from @RegionDalarna, Patrik Ellström, Johan Lindh and René Kaden from the Department of Medical Sciences at Uppsala University and Uppsala University Hospital. 🧵10/10
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Jonathan Haars @jonathanhaars.bsky.social · 29/05/2025
The manuscript was written together with my co-supervisor Johan Lennerstrand and co-authors Navaneethan Palanisamy from Chester Medical School, Frans Wallin, Paula Mölling and Martin Sundqvist from Örebro University, and… 🧵9
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Jonathan Haars @jonathanhaars.bsky.social · 29/05/2025
The threat to global health by SARS-CoV-2, Covid-19 and long covid is not over. Continual surveillance through sequencing is needed to understand the dynamics of its spread and evolution. 🧵8
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Jonathan Haars @jonathanhaars.bsky.social · 29/05/2025
This highlights the importance of rapidly developing, testing and approving new drugs for viruses undergoing relatively rapid evolution, such as SARS-CoV-2 because of its large global spread. 🧵7
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Jonathan Haars @jonathanhaars.bsky.social · 29/05/2025
We found that the lineages and mutations causing resistance became more common during the study period. Meaning these monoclonal antibodies may be less useful than initially thought. 🧵6
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Jonathan Haars @jonathanhaars.bsky.social · 29/05/2025
Among these drugs are the monoclonal antibodies. Which are very important to some of the most vulnerable people in society, the immunocompromised. We investigated how common the SARS-COV-2 lineages and mutations which offer resistance were in central Sweden in 2023 and 2024 🧵5
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Jonathan Haars @jonathanhaars.bsky.social · 29/05/2025
Whole genome sequencing allows tracking mutations and how their abundance changes over time. These are important, they are responsible for how the virus spreads, for how the virus evades the immune system, and are also responsible for causing resistance against drugs. 🧵4
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Jonathan Haars @jonathanhaars.bsky.social · 29/05/2025
This has helped us track which variants of the virus are present in the population at different times. Waves of different variants come and go, spreading from one continent to the next. 🧵3
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Jonathan Haars @jonathanhaars.bsky.social · 29/05/2025
In a collaboration between Region Uppsala, Region Dalarna and Region Örebro we nanopore sequenced SARS-CoV-2 to track resistance mutations affecting monoclonal antibodies pemivibart and sipavibart #COVID19 treatments. 🧵2
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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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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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Jonathan Haars @jonathanhaars.bsky.social · 05/12/2024
Because it's November in Sweden. We don't get much sun right now. There are solar panels but they will never provide much during winter.
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