Emily Smith

Molecular Epidemiology 🧬🦠🧫

[Michael Osterholm PhD, MPH @mtosterholm]

An excellent series by our team at @CIDRAP

[Theo Sanderson @theosanderson]

Near Real-Time Genomic Characterization of the 2025 Sudan Ebolavirus Outbreak in Uganda’s Index Case: Insights into Evolutionary Origins
https://t.co/bSFkePjB3I

Rapid sequencing of the outbreak genome by team from the National Health Laboratory, MoH of Uganda, UVRI, and others.

[Emily Smith @EmilyAnne_Smith]

Incredible effort by the CIDRAP CWD team!

[CIDRAP @CIDRAP]

CIDRAP report highlights gaps, offers guidance for possible #CWD spillover into people, other species

This effort, the first of its kind, explores the potential for spillover and mitigation of related health and economic consequences.

https://t.co/jo9rF7XjQG

[Emily Smith @EmilyAnne_Smith]

Hopefully samples will be sequenced to help identify potential sources for those cats without exposure to raw milk, and to monitor ongoing evolution across different hosts!

[CIDRAP @CIDRAP]

Los Angeles County confirms avian flu in cat deaths as more cases suspected

The three cats with suspected infections don't have any known exposure to raw milk, and investigators are examining other potential sources, including raw meat.

https://t.co/ZAKzETiUpV

[Emily Smith @EmilyAnne_Smith]

Ollie and I would like to remind everyone today that public health saves lives 🦠📈🧬

[Emily Smith @EmilyAnne_Smith]

@RajlabN @0bFuSc8 Quick correction: E189K (H3 numbering, corresponds to E201K in sequential numbering) is an antigenic mutation, but the effect is not as large as seen previously with A160T (H3 numbering). Thanks to @jbloom_lab for following up and making this resource available!

[Emily Smith @EmilyAnne_Smith]

@RajlabN @0bFuSc8 I reassembled using CDC's IRMA and was able to get a higher-quality HA gene segment for EPI_ISL_19469203 (SRR30932425). It's clade 2.3.4.4.b. The E201K looks "real", but there's nothing to suggest impacts on functionality in the Deep Mutational Scanning data (site 189).

[Emily Smith @EmilyAnne_Smith]

Nice analysis on the recent human H5N1 cases from California!

[Bloom Lab @jbloom_lab]

Below is brief analysis of HA mutations in two recent cases of H5N1 influenza in humans w contact w dairy cattle in California.

Summary is that while virus continues to evolve, nothing about HA mutations in these human cases is obviously alarming.

[Emily Smith @EmilyAnne_Smith]

@RajlabN XBB at 5% in the US? And 75% in region 5? I wonder if something's going on with lineage classification in the new pangolin version

[Emily Smith @EmilyAnne_Smith]

Nice thread on the sequence data from the recent H5N1 case from Missouri and associated limitations

[Emily Smith @EmilyAnne_Smith]

@shay_fleishon @AngieSHinrichs @SternLab Thanks for sharing this! Any thoughts on why the T14408C reversion is so common? Some sort of functional impact on RdRp?

[Pathoplexus @pathoplexus]

📢 We're excited to introduce Pathoplexus, a specialized sequence database for human viral pathogens! 🌍 🧬
Launching with 4 viruses, https://t.co/4wGez2nTCr combines modern open-source software with transparent governance to improve global pathogen sequence sharing.

1/14

[Delfina.Rana.Tortuga, PhD🏳️‍🌈⚽🔬☕ @DebWadford]

Congratulations to @RyderRahil and @EmilyAnne_Smith and all co-authors - great work reviewing sequence data for SARS-CoV-2 recombinants in California!! @VirusesMDPI
https://t.co/3rQ1KX6XzI

[Emily Smith @EmilyAnne_Smith]

Great statement from the American Association of Avian Pathologists on the inadequate response to H5N1 (B3.13) in dairy cattle, and improvements needed to protect poultry and human health https://t.co/EMeACiSVw3

[Dr. Angela Rasmussen @angie_rasmussen]

The answer to his question is simple.

You can’t stop transmission when you don’t know where the virus is.

That’s why we keep seeing cases.

That’s why this outbreak is not containable, at least given the current response.

That’s why we will see more cases going forward.

[Emily Smith @EmilyAnne_Smith]

@RajlabN I’m glad to see more sequencing and data sharing of H5N1 from wild birds!

[Theiagen Genomics @theiagen]

Interested in joining our team? We currently have several positions open, but we'll be closing them soon.

Learn more here: https://t.co/Y981XYlzlK

#Bioinformatics #Informatics #DataScientist

[Emily Smith @EmilyAnne_Smith]

@JosetteSchoenma @RyderRahil @nzm8qs @CorneliusRoemer Some genomes were rejected by GISAID, most commonly due to false frameshifts seen in ONT data

[Emily Smith @EmilyAnne_Smith]

Check out this recent preprint on SC2 recombinants to learn more about their detection and characterization, as well as associated challenges for public health labs! We welcome any feedback as this goes through the peer review process👩🏻‍💻

[Rahil Ryder @RyderRahil]

Excited to share our preprint on SARS-CoV-2 recombinants in California.

https://t.co/weCPkYp5L7

[Emily Smith @EmilyAnne_Smith]

@JosetteSchoenma @RyderRahil @nzm8qs @CorneliusRoemer Thanks for the feedback! Github issues weren't made for novel recombinants with smaller numbers, the reasoning being that they likely wouldn't recieve a lineage assignment with so few seqs. I typically use this approach when identifying novel recombs: https://t.co/UtZtTSu3xm