Amanda Warr

OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis. #StructuralVariants #SVs #SVcomparison #SVidentification #Bioinformatics 🧪🧬 🖥️
academic.oup.com/bioinformati...

Spider: a flexible and unified framework for simulating spatial transcriptomics data. #SpatialTranscriptomics #DataSimulation #Genomics #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...

I can say that having been working on this for a while, my cats have insurance in place specifically chosen to cover that cost just in case.
There are several international groups working on prevention and treatment for FCoV-23, so hopefully they should have solid data to share in the near future.

GS-441524 is the recommended treatment and has been used successfully in cases of FCoV-23. Unfortunately it is not available for veterinary use in every country, and is expensive. Molnupiravir was used during the outbreak in Cyprus as there were COVID stocks the government allowed use of.

Black cat draped elegantly over a beanbag foot stool

Also, my black cat says hi to your black cat.

I borrowed that tree as I'm on my phone and it was easier than finding my own! The source of that tree is this chapter, which may be of interest. But simply put, they're quite different. www.sciencedirect.com/topics/immun...

A phylogenetic tree showing alphacoronavirus-1 circled in red, and SARS-CoV-2 circled in blue, at opposite ends of the tree.

While this is about a coronavirus, it's not about that coronavirus. They're not very closely related, and while we did see cases of cats catching SARS-CoV-2, it isn't going to give your cat deadly FIP. Most cats that catch SARS-CoV-2 have very mild or no respiratory symptoms.

Loss of FCoV-23 spike domain 0 enhances fusogenicity and entry kinetics - Nature The molecular mechanisms of cell entry for the recently identified highly pathogenic feline coronavirus FCoV-23 are characterized in detail.

Important insights into FCoV-23 cell entry from the @veeslerlab.bsky.social

Freely available: www.nature.com/articles/s41...

Grok 4 seems to consult Elon Musk to answer controversial questions | TechCrunch Elon Musk's newly launched AI chatbot, Grok 4, seemed to reference Musk's posts on social media before answering controversial questions.

Grok 4 appears to consult Elon Musk's X posts and news about him when addressing controversial subjects like immigration or the Israel-Palestine conflict. This design choice, aiming to align with Musk's views, raises questions about Grok's stated goal of being a "maximally truth-seeking AI."
#MLSky

I've once again failed to tag appropriately for the various sciency bluesky feeds. 🧪🧬🖥️ #ViroSky #VirEvol

screenshot of a figure from the article, showing the chimeric composition of FCoV-23, with FCoV-1 backbone and spike from CCoVII

A lab is not required to generate chimeric coronaviruses, with a spike of a different virus: they can emerge naturally ▫️1/2

(from newly published paper by Attipa & @amandatron89.bsky.social et al.; preprinted in 2023)
www.nature.com/articles/s41...

Also interesting that the deletion between TGEV and PRCV tracks so closely with the FCoV-23 deletion!

Coronavirus causes fatal disease outbreak in cats | The Roslin Institute | The Royal (Dick) School of Veterinary Studies A harmful strain of coronavirus has caused a fast-spreading outbreak of a harmful feline disease.

A hybrid coronavirus, formed of cat and dog coronaviruses, caused a severe outbreak of disease among cats in Cyprus, researchers found.

Their work, in Nature, showed how this new virus was able to cause widespread cases of Feline Infectious Peritonitis (FIP) among the island’s cats.

We know it has come up in other European countries, but overall testing rates are low. We are working on some easy diagnostics. So far we've not had reports of any massive die-offs in feral populations so that is a good sign, but it is possible it just hasn't met a good cat dense environment yet.

So there have been more confirmed UK cases, so far all imports, but there may be some local spread that we don't know of. It's difficult to know when essentially the same disease already exists in the country from "normal" FCoVs, we only tend to hear about the imports.

Loss of FCoV-23 spike domain 0 enhances fusogenicity and entry kinetics - Nature The molecular mechanisms of cell entry for the recently identified highly pathogenic feline coronavirus FCoV-23 are characterized in detail.

For more on the domain 0 deletion in the spike gene, see another paper, also out today in Nature, looking at how the deletion enhances fusogenicity and entry kinetics.

www.nature.com/articles/s41...

Loss of FCoV-23 spike domain 0 enhances fusogenicity and entry kinetics - Nature The molecular mechanisms of cell entry for the recently identified highly pathogenic feline coronavirus FCoV-23 are characterized in detail.

For more on the domain 0 deletion in the spike gene, see another paper, also out today in Nature, looking at how the deletion enhances fusogenicity and entry kinetics.

www.nature.com/articles/s41...

*our

I'm so not redoing the whole thread for one typo though 😅

As a side note, Nature including "Thank you for choosing to publish your work with us." In an acceptance email is wild. I'm not convinced we were the ones doing the choosing, but you're welcome?

Our fur raising findings pose important questions about this novel virus and its potential impact on cat populations, especially in areas with high numbers of feral cats. Better understanding of the virus is important for developing effective treatment and prevention strategies.

We also identified a host-specific deletion in the spike gene which may play a role in its virulence.

This new recombinant’s genome is primarily feline coronavirus I (FCoV-I), but the spike gene originates from a pantropic canine coronavirus II (pCCoV-II). It is unclear if the virus does not need to do an in-host switch to cause FIP, or if it is simply more likely to occur.

Typically, feline coronavirus causes no symptoms, most cats get it at some point without anyone noticing. However, occasionally in an unlucky cat an in-host mutation can trigger FIP, a disease that is fatal without costly antivirals. Large outbreaks are rare since FIP usually doesn't spread.

Following an outbreak of Feline Infectious Peritonitis (FIP) in Cyprus, we sequenced samples from infected cats using @nanoporetech.com sequencing and discovered a novel recombinant between feline and canine coronaviruses, FCoV-23.

I am paw-sitively thrilled to say that out latest work is out in Nature today!

#Virology #Genomics #Coronavirus #AnimalHealth #InfectiousDisease #Sequencing #FIP #FCoV23

www.nature.com/articles/s41...

a man is carrying a large rock on his shoulders . ALT: a man is carrying a large rock on his shoulders .

Me waiting for my extension request to be granted

Everyday painkiller made from plastic — by E. coli Study highlights potential for sustainable synthesis of paracetamol.

Wow! Scientists engineered E. coli to convert plastic waste (PET) into pain medicine paracetamol (acetaminophen or Tylenol) in under 24 hours with up to 92% yield.
www.nature.com/articles/d41...

#medsky #pharmsky 🧪

🚨 Join us for the Environmental Metagenomics course (Oct 13–17, online) with @oskolkov.bsky.social & @aroneys.bsky.social !

🔬 Hands-on training on read-based & assembly-based methods, MAGs, and integrating short & long-read @nanoporetech.com data.

shorturl.at/HOm6X

Chatbots — LLMs — do not know facts and are not designed to be able to accurately answer factual questions. They are designed to find and mimic patterns of words, probabilistically. When they’re “right” it’s because correct things are often written down, so those patterns are frequent. That’s all.

Guidelines for preventing and reporting contamination in low-biomass microbiome studies Nature Microbiology - In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize...

Hope this is useful - consensus statement "Guidelines for preventing and reporting contamination in low-biomass microbiome studies" rdcu.be/er3Io