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

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

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 …

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 …

My latest scientific article: pubmed.ncbi.nlm.nih.gov/41529381/ 🧪 #Science #Research #Viruses #Biology #Sequencing

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...

I am now on Mastodon as well if you prefer that social site: mastodon.social/@Jonathan_Ha...
#Mastodon #Research

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…

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...
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GitHub - Kirk3gaard/MicroBench: Overview of our data for microbial genomic benchmarking Overview of our data for microbial genomic benchmarking - Kirk3gaard/MicroBench

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.

Demultiplexed raw data is available at SRA and SARS-CoV-2 and Influenza A sequences are available at GenBank.
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Bring structure to your research - protocols.io A secure platform for developing and sharing reproducible methods.

A step-by-step protocol is available at protocols.io: DOI: dx.doi.org/10.17504/protocols.io.36wgqn825gk5/v1
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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.
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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.
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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!
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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.
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#Virology
#Metagenomics
#Science

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…

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...
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A co-speciation dilemma and a lifestyle transition with genomic consequences in Wolbachia of Neotropical Drosophila
#Drosophila

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

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...

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

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...

Link to the original research article: www.tandfonline.com/doi/full/10.... 🧪

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...

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

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...

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

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 ...

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

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#COVID19
#SARSCoV2
#PostCovid
#LongCovid
#PASC

doi.org/10.3389/fimm...

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...

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....
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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 ...

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...

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.
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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…
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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.
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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.
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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.
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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
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