Josh Levy

Gunman in Deadly C.D.C. Shooting Fixated on Covid Vaccine, Officials Say

The shooting at the CDC in Atlanta, which killed a police officer, followed the spread of false information around Covid vaccines and animosity directed at the agency, public health workers say.

www.nytimes.com/2025/08/09/u...

"Vought & his cronies are shitting bureaucratic nukes & wiping their asses with the Constitution. This Executive Order is egregiously unlawful. It is a flagrant attempt to kill scientific research & education & exact economic ruin in service of corruption & the erosion of democratic norms."

It’s been quite a while… but we’re glad to report our San Diego wastewater dashboard is back up and running!

Real-time, multi-pathogen wastewater genomic surveillance with Freyja 2 Case-based infectious disease surveillance is fundamental to public health, but is resource-intensive, logistically complex, and prone to sampling bias. Wastewater testing and sequencing have increasi...

@kevinlibuit.bsky.social & @curtiskapsak.bsky.social were two of the co-authors on a new paper on Freyja 2 — a bioinformatics tool for real-time, multi-pathogen wastewater surveillance.

Read about it here: www.medrxiv.org/content/10.1...

Childhood Vaccination Rates Have Dropped Again, C.D.C. Data Shows

New federal data shows that vaccination rates among American children entering kindergarten fell during the 2024-25 school year, extending a worrying trend that began during the Covid-19 pandemic.

www.nytimes.com/2025/07/31/h...

Home - Modjadji

Lots more to come on that, and on the deployment of Freyja at the global scale soon! For more info on Freyja and Modjadji:

github.com/andersen-lab...

modjadji.info

We’re continuing to expand the number of pathogens we support for Freyja (github.com/andersen-lab...), and developing corresponding low-cost and highly sensitive amplicon sequencing schemes as our Modjadji initiative (including @scalene.bsky.social ‬ and @chris.primalscheme.com

Although the metadata is far from perfect, we find that many samples contain multiple sub-lineages, and that this diversity increases as you’d expect milk < bulk tank < retail.

For H5N1, we used publicly available milk sequencing, contributed by USDA and academic labs across the US, derived from “milk” from individual cows, to “bulk tanks” with milk from many cows, up to “retail milk” with milk from many cows and many farms.

We deployed this approach to track MPXV in Germany and Influenza A/H5N1 sequencing in the US from 2022 and 2024. While we found MPXV sequencing didn't recover lineage mixtures, Freyja 2 uncovered candidate sublineages (not resolvable due to low genomic coverage) that were likely circulating.

Our next step was to generalize this approach to other pathogens. To do this, we built workflows to extract lineage-defining mutation definitions, and convert those into “barcode” format for Freyja use. We’ve done this for MPXV, RSV, H5N1, and more, and our workflow is freely available.

We also incorporated a method to calculate lineage-specific growth advantage from longitudinal wastewater sequencing. Using data collected as part of SEARCH efforts in San Diego, we found Freyja 2 recovers growth advantages including for JN.1 that match literature results from clinical estimates.

We find these improvements drastically reduce the number of false positives, improve accuracy, and overall provide a more realistic portrayal of the data on hand, and what can be claimed about it.

Noting the many approaches and platforms used to sequence SARS-CoV-2 in wastewater, we established functionality that accounts for incomplete coverage in sequencing (making some lineages indistinguishable), and adaptive regularization that allows for Freyja 2 to account for empirical error rates.

Working with awesome groups like Theiagen and STaPH-B, we made Freyja 2 accessible to a broad range of users, including through drag and drop automated result generation via Terra/Galaxy (great for labs with limited bioinformatics experience), conda, and Docker containers.

Now to the paper: By leveraging the wealth of amazing resources for tracking the evolution of SARS-CoV-2, we established automated pipelines that keep analyses in line with the most recent pango designations, and allow users to access that information effectively immediately.

Freyja has become widely used for tracking of SARS-CoV-2 dynamics in public health labs across the world, we've slowly introduced lots of new features- often as a result of community feedback, so many thanks to all who have reached out via email/github issues/ slack over the past few years!

Real-time, multi-pathogen wastewater genomic surveillance with Freyja 2 Case-based infectious disease surveillance is fundamental to public health, but is resource-intensive, logistically complex, and prone to sampling bias. Wastewater testing and sequencing have increasi...

A few days ago we preprinted our Freyja 2 paper, describing the expansion of our original Freyja method to a real-time, multi-pathogen surveillance tool to track pathogen lineage prevalence and dynamics from sequencing of wastewater and other complex samples (like milk). 🧵
 doi.org/10.1101/2025...

The NIH’s 2024 budget of just under $37B generated $95B in economic activity in 2024 alone. 99.4% of new pharmaceuticals approved from 2010-2019 came from NIH-funded research. I’m hard pressed to think of anything that generates as much direct economic benefit as our NIH did before they destroyed it

What do you know, Mother Nature is up to her usual gain-of-function virology tricks again and is making new coronaviruses in wild Australian bats.

I think it's safe to say that we're probably in the beginning of what will become this summer's COVID-19 wave(let) - and if I had to take a guess, likely a relatively mild one.

This is based on test positivity, wastewater surveillance from SSI Denmark and US CDC. All 📈.

Links below.

About - Andersen Lab Learn more about the Andersen Lab, as well as jobs and career opportunities.

Are you looking for a Postdoc or Research Programmer position? Want to work as part of highly collaborative infectious disease programs that have direct relevance to global health?

Well, we got you covered!

Learn more 👇

andersen-lab.com/about/

I know RFK Jr. has assembled a quack crew to concoct a study showing otherwise but here is an new important large cohort study of over 1.2 million children in Denmark showing no association Aluminum adsorbed vaccines and chronic dz in childhood including autism.
www.acpjournals.org/doi/10.7326/...

Because disinformation & lies have drowned out experts like Dr. Titanji and her colleagues who provide evidence-based clinical care vs and who genuinely care about people’s health. Flooding the zone with bullshit drowns truth.

We need to stop playing defense & start fighting the propagandists.

Absolutely astounding paper about a recombinant feline-canine coronavirus. What is so fascinating is how the canine coronavirus spike gene recombines into the feline coronavirus. The breakpoints so closely track the gene.... it's just remarkable selection.

Summary Table of the massive defunding of biomedical research in the United States
www.nytimes.com/interactive/...

🚨 MEASLES OUTBREAK IN U.S.: WORST YEAR SINCE DISEASE WAS ERADICATED

A disease once eliminated in the U.S. is now roaring back. And we just hit a chilling milestone.

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Cambodia has confirmed its 9th and 10th human cases of H5N1 bird flu this year. 6 of these cases occurred in June alone. Sadly, 6 people have died in 2025. 🧪🧬🦠🔬🥼😷🐓💉

Destroying institutions and programs that drive American innovation, give hope to the sick and their families, and support the most vulnerable Americans.

And for what? Tax cuts for the rich, masked police with limited accountability, and a bigger deficit.

Horrendous.

Quick thread on the WHO's SAGO report on the origins of COVID-19, highlighting key points and even *new* data.

Their summary is that a zoonotic origin of COVID-19 is best supported by available data. This is consistent with most scientific reviews and statements in the rest of the literature.