Fascinated about virus evolution. Working on SARS-CoV-2. PostDoc at the Institute of Virology @Uniklinik_Fr
Freiburg Germany
Joined November 2021
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Jonas Fuchs retweeted
MEGA-CRISPR (multiplexed effector guide arrays) is an alternative to CRISPR editing that edits RNA instead of DNA. It swaps the DNA-cutting enzyme Cas9 for an RNA-cutting alternative called Cas13d. As mRNA doesn’t last very long in a cell, any potential mistakes disappear fast.
MEGA-CRISPR can shut down the production of multiple proteins, turning off up to 10 genes at once.
To showcase the power of this system, a new paper addressed a really important clinical problem: T cell exhaustion in immunotherapy treatment for cancer patients. What this means is that, when either natural or engineered T cells (such as in CAR-T therapy) are chronically activated too many times by a tumor for example, they lose their effectiveness and ultimately stop reacting.
The paper tunes exhaustion markers using an antibiotic switch of varying dose, creating a system that can essentially react dynamically and turn genes on/off as a function of a varying input.
This system is an important advance because
(1) editing mRNA is more versatile & less consequential than editing DNA
(2) it can edit very many genes at a time (up to 10)
(3) it can tune these many genes on/off using an external input
Exciting times ahead for cell therapies in oncology!
nature.com/articles/d41586-0…
Jonas Fuchs retweeted
Our case report of a fatal WNV infection in a travelling horse is now out in @EIDjournal... Get your horses vaccinated! @APHAgovuk
A fatal case of #WestNile virus occurred in a mare returning to the UK from Spain. The mare had no record of having received WNV vaccine.
Learn more in this February 2024 EID journal article:
bit.ly/3Su8qQw (Authors: Mirjam Schilling, et al.) @MirjamSchilling
Jonas Fuchs retweeted
We find DNA/RNA contamination in seq data, seq collections, & asssemblies. Either from biological sources, spike-ins, unwanted targets.
We provide an easy-to-use @nextflowio pipeline for reference- and mapping-based decontamination, latest release:
github.com/rki-mf1/clean/rel…
Jonas Fuchs retweeted
I am happy to finally announce the release of #Snakemake 8.0! In about half a year, we have modernized large parts of the code base. Most importantly, Snakemake 8.0 introduces a versatile plugin system, redesigned support for external storage, and modernized documentation. (1/n)
Jonas Fuchs retweeted
From Influenza A to an incredible diversity of viruses - great comprehensive analysis of Orthomyxoviruses!
👉journals.asm.org/doi/10.1128…
Jonas Fuchs retweeted
Really happy to see our paper on SARS-CoV-2 evolution in the Omicron era out in @Nature Microbiology today.
I'd normally write a thread outlining our paper, but I've not felt well for a while & can't focus well enough to do much of anything. Will try to write one later.
How #SARSCoV2 is continuing to evolve in the Omicron era, by many of the guiding lights who have so diligently tracked this virus throughout the pandemic
nature.com/articles/s41564-0… @NatureMicrobiol by @CorneliusRoemer @PeacockFlu @DannySheward @LongDesertTrain @siamosolocani
Jonas Fuchs retweeted
#Sotrovimab therapy elicits antiviral activities against #Omicron BQ.1.1 and XBB.1.5 in sera of immunocompromised patients.
Congrats to @Timothee_B and colleagues for studying neutralizing and non-neutralizing antibody activities
sciencedirect.com/science/ar…
Jonas Fuchs retweeted
Want to calculate the "Percentage Of Conserved Proteins" for bacteria?
My little @nextflowio implementation of the original approach from Qin et al. 2014 now uses Diamond instead of Blast for the protein alignments (thx @GregoireMichoud for the PR!)
github.com/hoelzer/pocp
Jonas Fuchs retweeted
Our study showing that severe COVID-19 in the aged organism is caused by an age-dependently impaired type I and type II interferon response, is now available in @JExpMed! Congrats and thanks to all collaborators, especially to first author Julius Beer! @MartinSchwemmle
Advanced age is the most critical risk factor for severe #COVID19. Beer, @MartinSchwemmle, @sandpiper_89 et al demonstrate that the age-dependent exacerbation of disease is driven by a diminished innate & adaptive immune response bit.ly/3Luw1g4
@Uniklinik_Fr @UniFreiburg
Jonas Fuchs retweeted
Three new workflows for analysis of variation in Monkeypox. Use it to call variants, produce reports, and/or consensus sequences. All supported by free powerful infrastructure suitable for 1000s of samples galaxyproject.org/projects/m… #usegalaxy
Jonas Fuchs retweeted
UKHSA has detected four new cases of monkeypox – three in London and one in the North East of England 🧵Thread:
These cases do not have known connections to the previous confirmed cases announced on May 7 and May 14. Read more:
gov.uk/government/news/monke…
Jonas Fuchs retweeted
Super happy to share our latest preprint addressing the pathomechanisms of the age-dependent disease severity of COVID-19!
It was a great team effort over the last 1.5 years!
biorxiv.org/content/10.1101/…
Jonas Fuchs retweeted
Current phylogenetic tree of all de-duplicated Delta-Omicron GKA recombinants from GISAID.
nextstrain.org/community/DC-…
Most recent sample was collected on 28 Feb. Really low circulation in Denmark, France, Germany, and the Netherlands.
Jonas Fuchs retweeted
We identified one 🇩🇪 SARS-CoV-2 genome that clusters w/ recent 🇫🇷 AY.4/BA.1 recombinants (99.7% nt ident, discussed at github.com/cov-lineages/pang…).
The seq marked in purple is the 🇩🇪 one we uploaded (GISAID: EPI_ISL_10910370). The tree just shows our internal seqID.
Jonas Fuchs retweeted
The lab of @MaesPiet has now confirmed the 1st case of B.1.1.529 in Belgium, with the other suspected case being an infection with the Delta variant. Returning traveler from Egypt, pointing to more widespread infections.
Jonas Fuchs retweeted
Just finished installing a new whisky cabinet in my office. Some say it’s the only @illumina whiskey cabinet in the world…
Jonas Fuchs retweeted
Preprint! Report on the hitherto rarely described SC2 lineage A.27, increased in spring '21 in sw GER but declined w/ Alpha rising.
HUGE wet lab work by the leading Jonas Fuchs & team! And great phylogeo checks by @evogytis @GuyBaele
and many others!
researchsquare.com/article/r…