So nohuman now ships an unmasked HPRC.r2 DB by default, with optional dataset selection. If you’ve used nohuman before, I highly recommend updating to v0.5.0 and re-downloading the new DB. Repo: github.com/mbhall88/nohuman Keep your metagenomes clean 🧹🧬

Day 4 of the metagenomic virus discovery workshop is all about phylogenetics and virus evolution! Thanks to Eduan Wilkinson, Jackie Mahar and @spyroslytras.bsky.social @ceri-news.bsky.social

Go @eakarlsson.bsky.social knocking it out of the park at the @virus-metagenomics.bsky.social workshop at CERI in Stellenbosch.

Tomorrow evening we have our keynote lecture session from 16:00 in the Neelsie Cinema, Stellenbosch University. Dr Maja Vukovikj will be speaking about Africas ancient disease landscape and Dr Erik Karlsson will talk about metagenomics and high-risk interfaces tinyurl.com/ytj3sppm

Viruses and bacteria jumping from animals to people became a real problem when humans started keeping livestock, according to a massive genomic analysis of ancient pathogens 🧪

First isolation of a mammalian chuvirus, bizarrely from Tasmanian Devil facial tumour cells. Work led by @julienmelade.bsky.social and @erinharvey.bsky.social. www.sciencedirect.com/science/arti...

academic.oup.com/cid/article-... This is a disappointing but predictable outcome of doxyPEP to prevent STIs. Drives AMR not only in Gonococcus, but in Staph aureus and Group A Strep.

Great session this morning at #ESCMIDGlobal 2025 discussing the use of whole genome sequencing in outbreak resposne. We have amazing scientific tools and should use them to better define and characterize outbreaks

Happy days at @escmid.bsky.social Global 2025 Vienna, presenting our posters on HDV and RSV epidemiology and viral metagenomics for community flu-like illness. Nice to meet the @esgrev-escmid.bsky.social committee too!

Another zoonotic (alpha) coronavirus. Closely related to the rodent virus AcCoV-JC34 that contains a putative furin cleavage site. www.tandfonline.com/doi/full/10....

@tstinear.bsky.social discusses the expansion of the very successful Austrakka to “Pathogen Trakka” which will enable secure, consistent sharing of microbial genomics data within LMICs and enhance access to bioinformatics/ visualisation tools. Looks like a winner! At Institut Pasteur New Caledonia.

Scientists, clinicians and public health from across the Pacific are discussing pathogen genomic surveillance at the Institut Pasteur de Novelle Caledonie at the stunning Pacific Community Building in Noumea. Here, @eakarlsson.bsky.social leads a discussion of wet lab technical requirements.

New preprint on canine viromes in Australia led by @jonathonmifsud.bsky.social. Includes the first RNA virus reported in dingoes - an unusual rotavirus A. Domestic dogs worldwide seem to carry a pretty similar set of viruses. www.biorxiv.org/content/10.1...

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I will not hide my inner convictions anymore. Be the change you want to see in the world ! #AcademicSky 🧪

It is time for "...routine use of diagnostic mNGS testing for hospitalized patients with suspected CNS infection." www.nature.com/articles/s41...

journals.asm.org/doi/10.1128/.... This is another “fail” for poorly selected CSF samples for clinical metagenomics - with low yields, even fewer changes in patient management/antibiotics. Metagenomics on plasma samples however performed very well - looks like a good target for BSIs and beyond.

Florian Krammer unpacks the entire history of human influenza viruses at OPTIONS XII in Brisbane.

We and others have been subject to relentless harassment. Here Nickels presents "supporting evidence" for our origins cover-up and we're not even discussing origins...we're discussing the lack of available SARS2 sequence data for surveillance.

A routine clinical metagenomics service using nanopore sequencing @ St Thomas' Hospital ICU🇬🇧 performed extremely well - 93% sens and 94% spec cf. routine microbiol testing. Median turnaround time = 6.7h. This is the beginning of the end of conventional microbiology. pubmed.ncbi.nlm.nih.gov/37938162/