I am very sad to hear of the passing of Professor Nicholas White, who has done so much to improve the treatment of malaria in his long and distinguished global career. Vale. www.tropicalmedicine.ox.ac.uk/news/profess...

Professor Sir Nicholas White OBE KCMG FRS

The Centre for Tropical Medicine and Global Health, the University of Oxford and the Nuffield Department of Medicine greatly mourn the death of Professor Sir Nicholas White, a distinguished clinician ...

tropicalmedicine.ox.ac.uk

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 🧹🧬

GitHub - mbhall88/nohuman: Remove human reads from a sequencing run

Remove human reads from a sequencing run. Contribute to mbhall88/nohuman development by creating an account on GitHub.

github.com

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 🧪

Animal diseases leapt to humans when we started keeping livestock

When hunter-gatherers began living close to animals, the pathogens that cause the plague and leprosy got closer too.

nature.com

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...

Isolation of an infectious mammalian chu-like virus from tumor cells of the endangered Tasmanian devil (Sarcophilus harrisii)

Jingchuvirales are single-stranded negative-sense RNA viruses classified into five families, including the Chuviridae.1 Jingchuviruses were first foun…

sciencedirect.com

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....

Novel human coronavirus in an infant patient with pneumonia, Republic of Korea

Coronaviruses (CoVs) pose a significant threat to public health, causing a wide spectrum of clinical manifestations and outcomes. Beyond precipitating global outbreaks, Human CoVs (HCoVs) are frequ...

tandfonline.com

@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...

Diverse Viral Pathogens in Australian Canines: Limited Geographic Structure and the First Detection of an RNA Virus in Dingoes

Viruses impose a substantial disease burden on dogs and the close relationship between dogs and humans may facilitate zoonotic disease emergence. Australia's geographic isolation, strict biosecurity m...

biorxiv.org

💪

Ilan Schwartz@germhuntermd.bsky.social · 2y ago

HIV/AIDS and COVID-19: Shared Lessons from Two Pandemics Anthony Fauci and Greg Folkers @cidjournal.bsky.social #IDSky academic.oup.com/cid/advance-...

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

www.cnn.com/2024/11/16/h...

United States’ first known case of more severe strain of mpox confirmed in California | CNN

The United States’ first known case of a more severe strain of mpox was confirmed in California, the US Centers for Disease Control and Prevention said Saturday. The risk of clade I mpox to the public...

cnn.com

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

Seven-year performance of a clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections - Nature Medicine

Next-generation metagenomic testing increases the accuracy and sensitivity of the etiology of central nervous system infections in hospitalized patients.

nature.com

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.

A retrospective observational study of mNGS test utilization to examine the role of diagnostic stewardship at two academic medical centers | Journal of Clinical Microbiology

Metagenomic next-generation sequencing (mNGS) stewardship practices remain poorly standardized. This study aims to provide actionable insights for institutions that seek to reduce the unnecessary usag...

journals.asm.org

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/

www.nature.com/articles/d41...

ChatGPT use shows that the grant-application system is broken

The fact that artificial intelligence can do much of the work makes a mockery of the process. It’s time to make it easier for scientists to ask for research funding. The fact that artificial intelli...

nature.com