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Steph N. Seifert, PhD

@stephseifertphd.bsky.social

1.7K followers 390 following 40 posts

PI of the Molecular Ecology of Zoonotic and Animal Pathogens Lab Co-PI, Viral Emergence Research Institute Interested in virology, evolution, ecology, and still cares about diversity and equity in STEM she/her

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Steph N. Seifert, PhD @stephseifertphd.bsky.social · Jul 14

🚨 Our team just released a reproducible Docker pipeline for RNAseq assembly and annotation designed for nonmodel organisms!

We're using it to explore how bats manage viral infections, but it's built for broad utility in wildlife transcriptomics. @viralemergence.org

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

TATAT: a containerized software for generating annotated coding transcriptomes from raw RNA-seq data

Motivation: Many transcriptome creation workflows are not standardized, are difficult to install or share, prone to breaking as dependencies update or cease to be maintained and are resource intensive...

www.biorxiv.org

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Reposted by Steph N. Seifert, PhD

Black Microbiologists Assoc (Black In Micro) @blackinmicro.bsky.social · 1d

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

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

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Noam Ross @noamross.net · 8d

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.

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raw9371 @raw937.bsky.social · 9d

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

Unlocking the genomic repertoire of a cultivated megaphage - npj Viruses

npj Viruses - Unlocking the genomic repertoire of a cultivated megaphage

share.google

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Reposted by Steph N. Seifert, PhD

Arinjay Banerjee @banerjeelab.ca · 14d

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

Stunning work from the Chandran lab!

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

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Reposted by Steph N. Seifert, PhD

Arinjay Banerjee @banerjeelab.ca · 16d

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

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

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Reposted by Steph N. Seifert, PhD

Maya Juman @mayajuman.bsky.social · 16d

Super excited to finally share this! #CollectionsAreEssential

Colin Carlson @colincarlson.bsky.social · 16d

🦇🦠 New preprint - in a long-term effort led by the amazing @mayajuman.bsky.social, we've shown that the ML tools developed by @viralemergence.org let us efficiently screen museum collections for pathogens with pandemic potential

🎉🔓 www.biorxiv.org/content/10.1...

Museum collections and machine learning guide discovery of novel coronaviruses and paramyxoviruses

Natural history museum collections are valuable but underutilized resources for viral discovery, offering opportunities to test hypotheses about viral occurrence across space, time, and taxonomic grou...

www.biorxiv.org

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Reposted by Steph N. Seifert, PhD

Arinjay Banerjee @banerjeelab.ca · 18d

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

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

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Reposted by Steph N. Seifert, PhD

Spyros Lytras @spyroslytras.bsky.social · 19d

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...

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...

www.cell.com

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Reposted by Steph N. Seifert, PhD

Timothée Poisot @ctrlalttim.com · 21d

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

A Julia toolkit for species distribution data

peercommunityjournal.org

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Steph N. Seifert, PhD @stephseifertphd.bsky.social · 21d

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

Steph N. Seifert, PhD @stephseifertphd.bsky.social · 22d

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

Steph N. Seifert, PhD @stephseifertphd.bsky.social · 22d

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

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Steph N. Seifert, PhD @stephseifertphd.bsky.social · 22d

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 (!!)

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Steph N. Seifert, PhD @stephseifertphd.bsky.social · 22d

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.

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Steph N. Seifert, PhD @stephseifertphd.bsky.social · 22d

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...

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...

www.biorxiv.org

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Reposted by Steph N. Seifert, PhD

Colin Carlson @colincarlson.bsky.social · 22d

🚨 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...

"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"

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Reposted by Steph N. Seifert, PhD

John M. Drake @jdrakephd.bsky.social · 22d

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/...

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Reposted by Steph N. Seifert, PhD

Ricardo Rivero H. 💻🧬 @ricardoriveroh.bsky.social · 25d

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...

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...

vetmed.wsu.edu

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Reposted by Steph N. Seifert, PhD

Timothée Poisot @ctrlalttim.com · 28d

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...

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

www.pandemicactionnetwork.org

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Reposted by Steph N. Seifert, PhD

arsweeny.bsky.social @arsweeny.bsky.social · 28d

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.

Colin Carlson @colincarlson.bsky.social · 29d

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...

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

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Reposted by Steph N. Seifert, PhD

Colin Carlson @colincarlson.bsky.social · 29d

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Jeremy Berg @jeremymberg.bsky.social · Sep 8

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.

1/2

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Reposted by Steph N. Seifert, PhD

Laboratory of Functional Viromics (LETKO) @fviromics.bsky.social · Sep 6

🧐 if you know, then you know

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

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 '' .

media.tenor.com

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Laboratory of Functional Viromics (LETKO) @fviromics.bsky.social · Sep 4

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)

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...

tinyurl.com

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Reposted by Steph N. Seifert, PhD

Nick Boyd @nboyd.bsky.social · Sep 2

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...

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