Steph N. Seifert, PhD

The summarised schedule of Black in Micro Week 2025, October 14-16. All times are in Eastern Standard Time. Mon 14: Pathways for Change. Welcome and Keynote Address 12pm. Marian Johnson-Thompson, PhD. Panel Discussion: Finding Black Spaces in STEM, 1:15-2:15 PM. Weds 15, Careers & Research: ECR Symposium 9-12 PM. Panel discussion: Navigating Careers in Microbiology 2-3 PM. Thurs 16, Community: Panel Discussion - Empowering Your Science 12-1:15 PM. Workshop: Science in Action

Friendly reminder: 🎉 Pre-register today & get ready to join our FREE online celebration. Everyone is welcome. To keep #BlackInMicro alive Donate: tinyurl.com/GiveBiM and Register to attend: linktr.ee/BlackInMicro (see links in bio) #BiMWeek2025

I have the privilege of working with fed agency folks. They've been jerked around, forced to move, had offices taken, lost resources, put on leave, fired, re-hired, *shot at*, and now furloughed. Still they return each day to help make America a bit more informed, healthier, and safer.

Multiomic analysis of the only megaphage in culture. In press today.

Unlocking the genomic repertoire of a cultivated megaphage | npj Viruses share.google/HgU1cjRnaHWv...

#phage #bacteriophage

LRP8 is a receptor for tick-borne encephalitis virus - Nature LRP8, an apolipoprotein E and reelin receptor with high expression in the brain, is a receptor for tick-borne encephalitis virus.

www.nature.com/articles/s41...

Stunning work from the Chandran lab!

Bats live with some viruses. But others can do them in Bats can carry some deadly human pathogens without signs of illness. A new survey shows that other viruses can still be bad for bats.

www.sciencenews.org/article/bats...

Super excited to finally share this! #CollectionsAreEssential

MERS-CoV and SARS-CoV-2 infection in diverse human lung organoid-derived cultures | Journal of Virology The COVID-19 pandemic heralded the upsurge in human-derived lung organoid-based studies due to their cellular heterogeneity that partly emulates the cellular complexity of the respiratory tract. A maj...

journals.asm.org/doi/10.1128/...

Molecular basis of sarbecovirus evolution and receptor tropism in natural hosts, potential intermediate hosts, and humans Kosugi et al. elucidate sarbecovirus evolution and ACE2 receptor tropism in natural hosts (12 Rhinolophus bat species), potential intermediate hosts (civets and raccoon dogs), and humans using a pseud...

Great to have this one published @cp-cellreports.bsky.social !! Some sarbecoviruses can use more ACE2 orthologs than others. The reason? A few sites in the RBD modulating the receptor usage of these viruses throughout their evolution! Worth a read 👇👇👇

www.cell.com/cell-reports...

Our software paper on SpeciesDistributionToolkit.jl is now published in @peercomjournal.bsky.social - peercommunityjournal.org/articles/10....

A single freezer inventory document that everyone must use, especially for samples! Each box has a specific position in the freezer, labeled as the location which has allowed us to recover from a freezer failure without everyone losing track of the boxes they need to find

One of the best parts of being at a land-grant university is the chance to connect field ecology, lab virology, and public health right here in our own community. Proud to contribute local science to global questions. @wsuvetmed.bsky.social

Huge shoutout to our co-first authors:
Grant Rickard (Undergraduate researcher now MD student) and Ricardo Rivero (PhD candidate) @ricardoriveroh.bsky.social
and many collaborators and local farmers who made this work possible 💫
@viralemergence.org

Timely as earlier this year, Whitman County reported a fatal case of HPS allowing us to share surveillance data with local & state Public Health partners. Even with our limited sample size, we detected viral reassortment and recovered two SNV genomes from voles (!!)

Last year, Whitmer et al. (CDC) highlighted a striking gap: a complete lack of SNV genomic data from the Northwestern US. Our small study begins to fill that gap, focusing on rodent surveillance in an agricultural region of Washington & Idaho.

First Sin Nombre virus (Orthohantavirus sinnombreense) genome sequences from the Northwestern United States We report the first Sin Nombre virus (SNV) genome sequences from the Northwestern United States and the first SNV sequences recovered from voles. Analysis of samples collected from 189 individual rode...

Excited to share our study reporting the first Sin Nombre virus (SNV) genome sequences from the Northwestern U.S., and the first ever from a vole host.

www.biorxiv.org/content/10.1...

"Health losses attributed to anthropogenic climate change," a brief communication in the journal Nature Climate Change. There's a map showing regions of the world, and pie charts of relevant studies as they apply to different health impacts like "heat-related deaths" and "maternal and child health"

🚨 NEW: Climate change is already causing 30,000 deaths per year - a global annual economic loss of $100-350B USD - but the true damage is probably 10x higher. Out TODAY in Nature Climate Change: the first systematic look at the science of "health impact attribution" 🔓 www.nature.com/articles/s41...

How do human-wildlife interfaces and seasonality interact during disease emergence? Our team has created a model, inspired by the #spillover of #Ebola, to better understand the interplay.

Read more about our research: royalsocietypublishing.org/doi/10.1098/...

Q&A with graduate student Ricardo Rivero WSU graduate student Ricardo Rivero is working to uncover the rules that govern how viruses evolve — insights that could one day help predict viral behavior and guide public health responses. A PhD st...

Honored to be featured in WSU’s “Q&A with a Graduate Student.” I talk about my path, current work, and the role of mentorship (special mention to my PI, @stephseifertphd.bsky.social) and collaboration in advancing my research goals. Full Q&A: vetmed.wsu.edu/qa-with-grad...

Briefing Paper on Pathogen Access and Benefit Sharing (PABS) | Pandemic Action Network

The @panaction.bsky.social just published a fantastic briefing paper about the Pathogen Access and Benefit Sharing system - take a look if you want the full perspective on what PABS is, and why it matters for both health equity and fair data governance.

www.pandemicactionnetwork.org/news/briefin...

Delighted to have this preprint out! It's been a long time in the works, involved a lot of fun discussion, and was a wonderful collaboration with Colin & Cecilia to get it from conception to final form.

Figure 3 of our paper, which shows viral coinfection networks at the virus level

New preprint! 🥳🎉 We looked at viral coinfection patterns at the largest scale ever in wildlife. We found a strong association among CoVs, PMVs, and influenza A, and higher coinfection rates in wildlife trade; plus, evidence that bats accumulate persistent infections. www.biorxiv.org/content/10.1...

Updating my analysis now that August data should be relatively complete.

Not great news...

The rate of investment of the appropriation is not increasing and it seems unlikely that the entire appropriation will be committed this year.

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a cat is petting a hedgehog in a black and white photo with the words `` happy hedgegie hugs '' . ALT: a cat is petting a hedgehog in a black and white photo with the words `` happy hedgegie hugs '' .

🧐 if you know, then you know

www.biorxiv.org/content/10.1...

Aminopeptidase N is a receptor for hedgehog merbecoviruses Merbecoviruses, closely related to the highly pathogenetic Middle East Respiratory Syndrome Coronavirus (MERS-CoV), circulate in hedgehogs throughout Europe and Asia, raising concerns about zoonotic t...

New preprint! If some merbecoviruses use DPP4 and others use ACE2, what do those hedgehog merbecoviruses use?! As it turns out, neither! In our latest study, we uncover the "missing" receptor for the MERS-related viruses in hedgehogs. [These findings were first shared at ASV this year] (1/6)

Recently tested some de-novo minibinders against two targets (thanks Adaptyv!) designed using our open-source design library, `mosaic`; our best method got hit rates of 7/10 and 8/10 and affinities as low as single-digit nanomolar. Wrote up some thoughts here: blog.escalante.bio/minibinder-d...

Reducing the threats of rodent-borne zoonoses requires an understanding and leveraging of three key pillars: disease ecology, synanthropy, and rodentation Rodents have co-existed with humans for centuries, and frequently exchange pathogens. Historically, rodent-driven plague outbreaks scoured the Old Wor…

New review out in @thelancetplanet.bsky.social from our rodent-borne zoonoses workshop @ciddpsu.bsky.social 🐭🌍

Humans & rodents share a long history and many pathogens -from plague to mpox. Outbreak prevention needs socially + ecologically grounded solutions

🔗 www.sciencedirect.com/science/arti...

Breakthroughs happen when diverse expertise is woven together. Collaboration can be messy—different vocabularies, different tools—but it’s worth it. We made a video with @MinuteEarth about it. 🎥 @fviromics.bsky.social @payeldas.bsky.social & Drew Kramer #EEID

Top: Experimental design depicting the passage experiment and the methods for quantifying infection prevalence, shedding ability, and infection prevalence in spillover populations. Middle: Host strains are ordered by the number of virus-positive plates over the course of the experiment (positive control C. elegans strain JU1580 set farthest right). Passage 0 denotes the exposure population. Note that the extraction procedure for passage 0 plates was different from the subsequent passages; many adult worms were removed from passage 0 populations to measure infection prevalence, intensity, and shedding (see methods). Bottom: Strains differed in epidemiological characteristics including B) maximum likelihood prevalence of infection, C) infection intensity (corrected median Ct), D) maximum likelihood shedding ability (the probability that 1 infected worm could cause visible fluorescence on a shedding plate), and E) relative susceptibility.

Will a #virus spillover into a new host species lead to dead-end infection or sustained #epidemic? This study uses a nematode-virus model to show that early #spillover traits, especially infection prevalence & shedding, are important predictors of viral persistence @plosbiology.org 🧪 plos.io/3UCnZHp

tskit_arg_visualizer: interactive plotting of ancestral recombination graphs Summary: Ancestral recombination graphs (ARGs) are a complete representation of the genetic relationships between recombining lineages and are of central importance in population genetics. Recent brea...

Excited to share our new preprint for the tskit_arg_visualizer Python package! ARGs can sometimes feel like a black box, so
@yanwong.bsky.social and I have been developing a method to programmatically drawing these graphs.

🔗 arxiv.org/abs/2508.03958

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The CDC shooting was public health’s Jan. 6 “In RFK Jr.’s America, it will never be safe to practice public health or medicine," write an epidemiologist and a former CDC staffer.

NEW 🚨 The violence is the point. Elected Dems must call for widespread resignations (RFK, Bhattacharya, Prasad) in response to the CDC shooting. Public health must demand this of them, and the public must demand that of us. With @publichealthguy1.bsky.social in STAT: www.statnews.com/2025/08/15/c...