1/ 🚀 Pathoplexus now supports the Andes variant of Hantavirus (ANDV). ANDV is the variant identified in the recent MV Hondius cases, & the Hantavirus variant previously identified as having occasional human-to-human transmission. pathoplexus.org/andv #hantavirus #hondius

Open question for anyone that develops/maintains of bioinformatics tools, especially those used for public health - what do you think is the right way to fund this long term? Grants are great for new research directions, but aren't really appropriate for most tool dev/maintenance.

1/ 🦟 Big news: #Pathoplexus now supports Dengue virus & Yellow Fever virus - two arboviruses responsible for over 400 million infections and up to 94,000 deaths per year. Here's what’s new in our latest update 👇🏻 Read the full update: pathoplexus.org/news/2026-03... 📰

@pratikkatte.bsky.social and I just released Lorax 🌲, a tool for interactive exploration of biobank-scale ancestral recombination graphs (ARGs). If you’ve ever wanted to scroll across the ancestries of thousands of genomes… this is for you.

In 2025, GISAID cut off access to many critical SARS-CoV-2 resources, incl. our outbreak.info. A month ago, GISAID leveled accusations against us, Cov-Spectrum, Nextstrain, and members of COG-UK, which are false and misrepresent known facts. Our joint response: blog.outbreak.info/joint-respon...

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social a) correcting errors in 4.5 million genomes & their phylogeny b) improving representation of the Global South in public data www.nature.com/articles/s41... (thread 1/n)

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods

This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

nature.com

RFK says basically every infectious disease came from a lab or vaccine.

We need a better way to get the 3800+ kids out of ICE detention than this. We know Liam’s name and we can advocate on his behalf, but that isn’t true of almost any of the other people stuck in detention centers. We have to stop ICE on a systemic level.

Phil Lewis@phillewis.bsky.social · 7mo ago

SAN ANTONIO (AP) — Judge orders US to release father and 5-year-old taken into custody during Minnesota immigration crackdown.

I am wondering if any of the loudest proponents of "learning loss" in the context of the COVID-19 pandemic have spoken up about what ICE is doing to students' ability to learn, safety, etc. I'll wait...I'm sure they're on it. www.chalkbeat.org/2026/01/28/e...

‘People are living in fear’: Education groups demand changes to immigration enforcement

Critics are pushing to condition funding for the Department of Homeland Security on changes to immigration enforcement agents’ aggressive tactics, like detaining parents and children on their way to s...

chalkbeat.org

This must be that radical transparency I keep hearing about.

Max Kozlov@maxkozlov.bsky.social · 7mo ago

I'm at the Willard Hotel where I've been denied entry and kicked out of the Reclaiming Science event with NIH director Bhattacharya & other top agency leaders. @jocelynkaiser.bsky.social and I registered for the event months ago yet were told capacity was full, even as they let in dozens of others.

The majority of organizing happening in Minnesota isn’t just peaceful, it’s INVISIBLE. Moms showing up who won’t be interviewed on TV, people whose ICE patrols don’t turn into viral video. The grocery runs, the donations, the people filming bc they happen to be there. Please remember this.

Yup - here's a good resource where they could pop the data right over: pathoplexus.org/measles/. And, it would take about a full two minutes to figure out how these outbreaks may be connected via e.g.,: nextstrain.org/measles/genome.

Pathoplexus | Measles Virus - Browse

Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

pathoplexus.org

This is the most astonishing graph of what the Trump regime has done to US science. They have destroyed the federal science workforce across the board. The negative impacts on Americans will be felt for generations, and the US might never be the same again. www.nature.com/immersive/d4...

An article today in @natmed.nature.com lays out a "New Vision" for NIAID, stating that following Covid "much of the American public lost trust in the NIAID, the National Institutes of Health (...), and in the greater scientific community" Let's have a look at what they cite in support of that 1/n

Just because the US is pretending that viruses only come from labs & we shouldn't bother with prevention otherwise, H5N1 is still here & is still a huge pandemic threat. Join me & my expert colleagues Mar 3-4 in DC as we figure out what to do about it. www.eventbrite.com/e/johns-hopk...

Today, Minneapolis. Tomorrow, it could be my town, your town, anywhere. The good news is that people in all the towns care about their neighbors and are organizing to resist this. It will stop when enough of us say no.

Laurel Krahn@windowseat.bsky.social · 7mo ago

Interview: www.youtube.com/watch?v=Inn-...

We are recruiting for a number of PhDs in the HPRU in Public Health Genomics, based at @unibirmingham.bsky.social, in collaboration with UKHSA. 🦠🧬 Apply below to work on cutting-edge science and public health priorities! (NB deadline of 9th January / UK only due to funding restrictions) (1/7)

As wastewater has become a core part of infectious disease surveillance worldwide, new guidance from WHO, GLOWACON, ASTHO, and others has laid key foundations for public health. But in practice, it’s not always obvious how to apply these recommendations or choose among available tools.

1/ 🚀 Pathoplexus now supports Marburg virus (MARV) and Ravn virus (RAVN) (sister viruses in the same genus). MARV has two main clades and causes severe disease with reported fatality rates of 24–88%. You can read more detail about adding Marburg here: pathoplexus.org/news/2025-11...

Hard day today Here's what we think about trusting CDC

The CDC website has been lobotomized. Where it once presented the decades of evidence debunking the false claims of a link between vaccines and autism, that has now been replaced with junk science.

Pathoplexus is growing not only in terms of new sequences, but also integrating into the larger ecosystem of pathogen surveillance by joining WHO's IPSN and expanding membership. This is the way a pathogen sequence database should work! (Lessons learned from GISAID/SARS-CoV-2...)

Pathoplexus@pathoplexus.org · 9mo ago

1/ 🚀 Big thanks to our community - since August we’ve added thousands of new sequences, rolled out major new features, and welcomed fresh faces into the #Pathoplexus world. Let’s dive into what’s new.👇🏻 Read the full update: pathoplexus.org/news/2025-11...

My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation. 4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.

Nextstrain@nextstrain.org · 10mo ago

On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5

Well, I suppose they renamed the Department of Defense to the Department of War, so probably about time to rename the Department of Health to the Department of Disease.

Dr. Lucky Tran@luckytran.com · 9mo ago

RFK Jr says he will end the "war" on saturated fats, contradicting decades of evidence-based dietary recommendations. "We’re ending the war on saturated fats in this country. So, we’re going to publish dietary guidelines that are going to stress the importance of protein and saturated fats."

If you have to get permission to teach in your area of expertise from people who are definitionally not qualified to adjudicate your expertise then you are no longer working at a university. You’re working at a state propaganda factory.

Phil Lewis@phillewis.bsky.social · 9mo ago

COLLEGE STATION, Texas (AP) — Texas A&M adopts policy requiring professors to get OK from school president to discuss certain race and gender issues.

🚨Dept. of Education proposes to exclude public health degrees from the “professional degree” category. That means new public health experts could lose access to key higher ed resources, like loan limits & reimbursement. A bold strategy to let infectious diseases win! 🦠 aspph.org/department-o...

Department of Education Proposal Excludes Public Health Degrees from “Professional Degree” Definition

Discover the new results and implications of Dept of Ed consensus regarding professional degree programs and public health education.

aspph.org

Defunding scientists for the nationality of who they co-author with or who they train. One of the most radical attack on freedom of speech in US history. A far right nationalist destruction of US science. Such a shameful time to be an American that this racist stupidity has become mainstream.

Roland Hatzenpichler@environmicrobio.bsky.social · 9mo ago

“The prohibited activities would include joint research, co-authorship on papers, and advising a foreign graduate student or postdoctoral fellow. The language is retroactive, meaning any interactions during the previous 5 years could make a scientist ineligible for future federal funding.”

🚨🚨 🧵1/6 #FedFam, reporters - urgent help needed 🚨CDC Museum (a Smithsonian affiliate) is being shuttered🚨 Staff are being “un-RIFed” just to close the museum permanently — then RIFed again in Jan This is bureaucratic cruelty & cultural vandalism CDC Library is a national treasure #SaveCDCLibrary

The David J. Sencer CDC Museum: In Association with the Smithsonian

Free museum exhibiting public health topics and the history of CDC.

cdc.gov

Like… people want affordable groceries, housing, and healthcare, *And* they want their friends and loved ones the be alive and safe and free from persecution. These are not mutually exclusive ideas. They are in fact bound up together.

Dr. Damien P. Williams is just… so tired.@wolven.blacksky.app · 10mo ago

Too many news outlets & pols framing Tuesday as affordability *Instead Of* "woke"/"DEI"/whatever the fuck when Mamdani & Sherrill both *explicitly* embraced trans & other LGBTQ+ rights, VA solidly rejected Republicans' virulent anti-trans attack adz, & a PA elected their 1st trans mayor. Be serious.

To back up their (incorrect) argument that COVID vaccines didn't affect transmission of the early variants, someone just sent me a paper showing that vaccines 'only' prevented infection... The thing is, it's pretty hard to transmit COVID if you don't get infected in the first place.