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Emily Anne Smith

@emilyanne-smith.bsky.social
516 followers 75 following 5 posts

Scientist at University of Minnesota Center for Infectious Disease Research & Policy (CIDRAP). Here for all things molecular epidemiology, public health policy, and cats.

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Reposted by Emily Anne Smith
Pathoplexus @pathoplexus.org · 22/09/2026
1/ 🧬 A big #Pathoplexus milestone: you can now optionally include raw sequencing reads alongside your consensus sequences! Hosting raw reads alongside consensus data helps improve reproducibility & allow in-depth analyses. 📰 Read more: pathoplexus.org/news/2026-09...
AI-generated image showing raw reads (short reads) lining up above a consensus sequence, with both the raw reads and consensus sequence labelled. Vague images below show a virus, coverage, and DNA.
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Reposted by Emily Anne Smith
CIDRAP @cidrap.bsky.social · 09/09/2026
📢 New publicly available resource for veterinary vaccine research: The Veterinary Coronavirus Vaccines Landscape The Veterinary Landscape includes more than 150 vaccines that are organized by: 🔬 Status 🦠 Virus/Disease 🐓 Animal group 🧬 Platform More: bit.ly/46ySN1P
Graphic titled, "Coronaviruses of Veterinary Importance". Graphic lists 4 coronavirus genera: Alphacoronaviruses, Betacoronaviruses, Gammacoronaviruses, and Deltacoronaviruses. Graphic is against a navy blue background and has the CIDRAP logo in the bottom right corner. Graphic titled, "Vaccines in Development or Available for Domesticated Animals in All Four Coronavirus Genera"
A pie chart is broken down into 5 categories: Alphacoronaviruses, Betacoronaviruses, Gammacoronaviruses, and Deltacoronaviruses with a 5th color code for "cross-genus". 

Graphic is against a navy blue background and has the CIDRAP logo in the bottom right corner. Graphic titled, "Platforms for Veterinary Coronavirus Vaccines in Development or Commercially Available"

The chart is color coded by "Inactivated", "Virus-like Particle", "Nanoparticle", "Protein Subunit", "Viral Vector", "Bacterial Vector", "mRNA", "circRNA", "saRNA", "Plant-based", "DNA", "Live-attenuated", and "Phage"

Chart is organized by 5 rows: Alphacoronaviruses, Betacoronaviruses, Gammacoronaviruses, and Deltacoronaviruses with a 5th color code for "cross-genus". 

Graphic is against a navy blue background and has the CIDRAP logo in the bottom right corner.
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Pathoplexus @pathoplexus.org · 27/08/2026
1/ 🎂 Pathoplexus turns TWO! 🎉 Two years ago we launched with an idea: what if pathogen data sharing put open access, speed, ease of use, & credit for data generators at its center? Here's what our community has built since: 📰 Read the full update: pathoplexus.org/news/2026-08...
AI generated watercolor-style image of a white birthday cake with blue and gold small decorate balls around the base and top, with a blue Pathoplexus logo on the side. On top, is a gold and white '2' candle that's lit. From the cake come strands of blue and gold, representing stylized DNA, network nodes, and ribbons representing credit and attribution.
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Pathoplexus @pathoplexus.org · 09/05/2026
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
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pha4ge.bsky.social @pha4ge.bsky.social · 05/02/2026
Kick off the first Genomic Horizons webinar of the year with @bede.im on “Practical panhuman host sequence depletion for responsible data sharing”. 📅 12 February 2026 ⏰ 14:00 – 15:00 UTC 🔗 Register here: bit.ly/4kiYW80
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Reposted by Emily Anne Smith
CIDRAP @cidrap.bsky.social · 17/12/2025
New! Public Health Alerts, a joint CIDRAP/NEJM Evidence effort to strengthen early detection and response to emerging health threats. First 2 reports: • Community transmission of clade Ib mpox in LA area • Flu virus characteristics and vax effectiveness data supporting WHO 2025–26 strain selections
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Emily Anne Smith @emilyanne-smith.bsky.social · 10/12/2025
Check out this thread highlighting our recent work on community-driven best practices in wastewater surveillance! It's been wonderful working with @josh-levy.bsky.social and the @pha4ge.bsky.social team to develop this user-friendly, open-source guidance🦠💧💩
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Nick Loman @pathogenomenick.bsky.social · 08/12/2025
Amazing novel mpox recombination between epidemic clade 1 and 2 in returning traveller detected in UK: virological.org/t/inter-clad...
virological.org
Inter-Clade Recombinant Mpox Virus Detected in England in a Traveller Recently Returned from Asia
Inter-Clade Recombinant Mpox Virus Detected in England in a Traveller Recently Returned from Asia Authors: Steven T. Pullan1, Isobel Everall1, Rebecca Doherty1, Lucy Crossman1, Emma Wise1, Hassan Ha...
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CIDRAP @cidrap.bsky.social · 02/12/2025
New review finds no evidence to support delaying universal hepatitis B birth-dose vaccination Analysis of over 400 studies ahead of ACIP mtg reveals no evidence that delaying the universal hepatitis B vaccine birth dose improves safety or effectiveness www.cidrap.umn.edu/c...
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Katelyn Jetelina @kkjetelina.bsky.social · 20/11/2025
For the first time in my career, I can’t tell people to trust what the CDC website says. And that is an incredibly sad and devastating place for this country to be.
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Nextstrain @nextstrain.org · 06/11/2025
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
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CIDRAP @cidrap.bsky.social · 06/11/2025
Next up for Vaccine Integrity Project: reviewing data on birth dose of hepatitis B vaccine The review will look at decades of data on the safety, efficacy, and public health impact of administering the hepatitis B shot at birth. www.cidrap.umn.edu/h...
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Isabella Eckerle @eckerleisabella.bsky.social · 29/10/2025
That would have been big news a few years ago, unfortunately the great science that gives important understanding in coronaviruses is now back to the small circle of scientists. Anyway: A fully functional furin cleavage site in a bat betacorarnavirus! Congrats to the authors!
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CIDRAP @cidrap.bsky.social · 30/10/2025
CIDRAP and CEPI launch resources to track development of coronavirus vaccines The revamped open-access site tracks scientific progress toward the development of broadly protective coronavirus vaccines www.cidrap.umn.edu/c...
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Emily Anne Smith @emilyanne-smith.bsky.social · 19/08/2025
The live stream of the Vaccine Integrity Project Evidence Base for 2025 Fall/Winter Immunizations starts in ~30 min!
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CIDRAP @cidrap.bsky.social · 15/07/2025
3 years in, #flu vaccine R&D project reports substantial progress The Influenza Vaccines Research and Development (R&D) Roadmap Initiative has accomplished 14% of its high-priority research goals and made progress on another 83%. www.cidrap.umn.edu/i...
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CIDRAP @cidrap.bsky.social · 17/06/2025
📢 ANNOUNCEMENT! CIDRAP's Vaccine Integrity Project has released an interim update and call to action. It outlines urgent, high-impact recommendations needed to protect public health. www.cidrap.umn.edu/v...
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CIDRAP @cidrap.bsky.social · 10/06/2025
Viewpoint: RFK's reckless firing of CDC #vaccine advisors not supported by evidence Kennedy's rationale is based on a series of inaccuracies and part of a pattern of misrepresentation. www.cidrap.umn.edu/c... Photo: CDC
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CIDRAP @cidrap.bsky.social · 22/05/2025
Low-cost genome sequencing project to expand beyond COVID The ARTIC 2.0 project will expand use of a low-cost, real-time genome sequencing technique used to detect COVID-19 variants to conduct surveillance on a variety of pathogens. www.cidrap.umn.edu/c...
cidrap.umn.edu
Low-cost genome sequencing project to expand beyond COVID
The ARTIC 2.0 project will expand use of a low-cost, real-time genome sequencing technique used to detect COVID-19 variants to conduct surveillance on a wider variety of pathogens.
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Pathoplexus @pathoplexus.org · 22/05/2025
📢Today Pathoplexus announces the inclusion of 2 new viral pathogens: RSV (A & B) and HMPV. These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response. 1/4
Screenshot of the homepage of Pathoplexus, showing tiles to navigate to the supported pathogens CCHF, Ebola Sudan, Ebola Zaire, HMPV, Mpox, RSV-A, RSV-B, and West Nile virus.
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Kristian G. Andersen @kgandersen.bsky.social · 27/02/2025
It is worth paying close attention to the new bill "Dangerous Viral Gain of Function Research Moratorium Act" introduced by Senator Roger Marshall. If enacted, it will effectively stop all of virological research, including for vaccines. www.marshall.senate.gov/wp-content/u... 🧵👇
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CIDRAP @cidrap.bsky.social · 19/02/2025
Canada announces avian flu vaccine buy as USDA confirms first H5N1 detections in rats Also, Canada's vaccine advisors issued preliminary guidance on use of the vaccine in high-risk groups. www.cidrap.umn.edu/a...
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Emily Anne Smith @emilyanne-smith.bsky.social · 19/02/2025
One of the most overlooked aspects of these mass layoffs is that in addition to these scientists being experts in their field, they had chosen to dedicate their career to public service. That matters. www.nytimes.com/2025/02/18/u...
nytimes.com
Trump Cuts Target Next Generation of Scientists and Public Health Leaders
A core group of so-called disease detectives, who track outbreaks, was apparently spared. But other young researchers are out of jobs.
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Angie Rasmussen @angierasmussen.bsky.social · 05/02/2025
New development: this is the first detection of genotype D1.1 H5N1 virus in cattle. All cattle sequences to date were genotype B3.13 & were all descended from a single spillover. New genotype means new introduction to cows from birds. www.statnews.com/2025/02/05/u...
statnews.com
USDA milk testing shows different strain of H5N1 bird flu in Nevada dairy herds
The USDA said four Nevada dairy herds were infected with an H5N1 bird flu strain that has circulated in wild birds, making prospects for containment in cows appear dim.
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 03/02/2025
First genome sequence from the Ugandan Ebolavirus outbreak with analysis: virological.org/t/990 and first filovirus genome submitted to Pathoplexus database: pathoplexus.org/seq/PP_0011C.... Great (and rapid) work from the National Health Laboratory, UVRI and partners.
virological.org
Near Real-Time Genomic Characterization of the 2025 Sudan Ebolavirus Outbreak in Uganda’s Index Case: Insights into Evolutionary Origins
Introduction Case History: On January 30, 2025, the Ministry of Health declared an outbreak of Sudan Ebola Virus (SUDV) Disease in Kampala, Uganda, following the death of a healthcare worker at Mula...
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