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
Jonathan Haars
@jonathanhaars.bsky.social
PhD-student in clinical microbiology at Uppsala University and Uppsala University Hospital, Sweden. Interested in Nanopore sequencing, metagenomics, SARS-CoV-2 and more.
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
My latest scientific article: pubmed.ncbi.nlm.nih.gov/41529381/ 🧪 #Science #Research #Viruses #Biology #Sequencing
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 …
pubmed.ncbi.nlm.nih.gov
My latest scientific article: pubmed.ncbi.nlm.nih.gov/41529381/ 🧪 #Science #Research #Viruses #Biology #Sequencing
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 …
pubmed.ncbi.nlm.nih.gov
I am now on Mastodon as well if you prefer that social site: mastodon.social/@Jonathan_Ha... #Mastodon #Research
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...
mastodon.social
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 🧪
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…
sciencedirect.com
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 - Kirk3gaard/MicroBench: Overview of our data for microbial genomic benchmarking
Overview of our data for microbial genomic benchmarking - Kirk3gaard/MicroBench
github.com
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 🧪
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…
sciencedirect.com
A co-speciation dilemma and a lifestyle transition with genomic consequences in Wolbachia of Neotropical Drosophila #Drosophila
A co-speciation dilemma and a lifestyle transition with genomic consequences in Wolbachia of Neotropical Drosophila #Drosophila
PubMed link
pubmed.ncbi.nlm.nih.gov
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
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
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
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...
physiciansweekly.com
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
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...
physiciansweekly.com
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
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...
link.springer.com
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...
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 ...
doi.org
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 🧪
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...
tandfonline.com
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...
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 ...
doi.org
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 🧪
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...
tandfonline.com
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
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
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...
link.springer.com
www.researchsquare.com/article/rs-5... 🧪
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...
researchsquare.com
www.microbiologyresearch.org/content/jour... 🧪
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...
microbiologyresearch.org
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
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...
pnas.org
This is the updated metagenomics protocol for respiratory samples search.app/V491AEp3tmB7...
Pan-microbial metagenomics protocol v1.2Public workspaceCritical
search.app
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 🧪
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
papers.ssrn.com
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...
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 🧪🦠🧬🔬🥼🥼🧑🔬
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...
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
