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)

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.

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...

This must be that radical transparency I keep hearing about.

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.

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.

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...)

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.

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.

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.

🚨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...

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.

🚨🚨 🧵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

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.

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.

Open position at the Swiss Institute of Bioinformatics: We are looking for a Director of the Center of Pathogen Bioinformatics apply.refline.ch/499599/0346/... I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and

I want to spell this out in case the implications aren't clear: This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited. The file allowed this. Cut that - cut off all tools the public & others were using.

Nextstrain's daily-updated tree of SARS-CoV-2 genomes was my gateway into the world of viral phylogenetics in early 2020, and Nextstrain's beautiful interactive tree display is crucial to making usher.bio results usable. GISAID cutting off data harms global surveillance efforts. 🧵👇

A List of Things Said to Have Been Ruined by Women 🧵

Colorado shows that feeding children is still a popular notion. All school meals should be free.

GISAID is now blocking genomic sequencing access to critical resources like Nextstrain, Covspectrum, Outbreak-info, & others. This makes us less safe, as live tracking of viral evolution remains critical for assessment of emerging threats. This needs to be escalated.

Since Greg Abbott made Houston remove the rainbow crosswalk. Rainbows are being painted on homes and businesses all over the city.

The USDA sent an email to grocery stores telling them they are prohibited from offering special discounts to customers affected by the SNAP funding lapse. I'm aware of at least 2 stores that had offered struggling customers a discount, then withdrew it after receiving this email

@andersonfbrito.bsky.social and I are seeking input from the community on hosting/sharing arbovirus sequencing data (DENV, CHIKV, OROV, ZIKV, & YFV) on @pathoplexus.org. Please consider filling out this VERY SHORT survey about your interest and/or concerns. docs.google.com/forms/d/e/1F...

You know the situation is bad when the national media is publishing guides to recognize which armed forces might be in your neighborhood. Trump is ensuring that all parts of the omniforce will be paid during the shutdown, unlike their civilian peers. donmoynihan.substack.com/p/the-risks-...

Finally read the paper and it's worth the buzz. mRNA vaccines saved 20 million lives in a global pandemic and the technology is opening up new avenues for the treatment of deadly cancers. This is really one of the most impactful scientific developments of our time. www.nature.com/articles/s41...

"Data shows that expansion of those who participate in academic science produces better science that has a wider impact." From a new research-backed defense of DEI programs published today by Needhi Bhalla @ucsantacruz.bsky.social and peers @ucsdmedschool.bsky.social and @uofmass.bsky.social 👏🏾👏🏼👏

🗓️ June 5, 1981: five cases of Pneumocystis Pneumonia, one report, a global awakening. 💙 The MMWR gave voice to what became the HIV/AIDS epidemic—and countless public-health moments since. 🕯️ Honoring the science and reporting that save lives. www.cdc.gov/mmwr/preview... #MMWR #CDCSavesLives

From a new @thelancet.com article today entitled "Health care in the USA: money has become the mission" www.thelancet.com/journals/lan...

The estimate of the Davis, CA #NoKings protest was over 4,500! #DavisCA

And now NextStrain as well. Next up, will GISAID start charging open-source community tools to have access? That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.

Our lab's first paper is out! Led by Jordan Ort, we developed NextClade datasets that enable rapid H5 clade assignment via NextClade. We deployed these during the start of the H5 cattle outbreak, and we finally published the paper in Virus Evolution academic.oup.com/ve/article/1...

Trump: "We're just at the start. We're going to go into other cities that we're not talking about purposely. We're getting ready to go in."

Awesome public health news: Maldives becomes the first country to achieve ‘triple elimination’ of 1. mother-to-child transmission of HIV, 2. Syphilis and 3. Hepatitis B www.who.int/news/item/13...