Emily Smith

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Emily Smith

Emily Smith

@EmilyAnne_Smith

Molecular Epidemiology 🧬🦠🧫

Minneapolis, MN Katılım Ağustos 2011
440 Takip Edilen1.9K Takipçiler
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Theo Sanderson
Theo Sanderson@theosanderson·
Near Real-Time Genomic Characterization of the 2025 Sudan Ebolavirus Outbreak in Uganda’s Index Case: Insights into Evolutionary Origins virological.org/t/near-real-ti… Rapid sequencing of the outbreak genome by team from the National Health Laboratory, MoH of Uganda, UVRI, and others.
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Emily Smith
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. cidrap.umn.edu/avian-influenz…

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Emily Smith
Emily Smith@EmilyAnne_Smith·
Ollie and I would like to remind everyone today that public health saves lives 🦠📈🧬
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Emily Smith
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!
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Emily Smith
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).
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Raj Rajnarayanan
Raj Rajnarayanan@RajlabN·
#H5N1 updates 10/10/2024 #DairyMilk surveillance is turning out to be a really good deal in forecasting what to expect (in terms of mutations and adaptation potential) Which we also get linked metadata asap along with the sequences.. HA mutations:
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Emily Smith
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
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Emily Smith
Emily Smith@EmilyAnne_Smith·
Nice thread on the sequence data from the recent H5N1 case from Missouri and associated limitations
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shay fleishon 🧬
shay fleishon 🧬@shay_fleishon·
Link to the latest update of the table of suspected chronic patients. Thanks to @AngieSHinrichs for the information that forms the basis for this analysis. And of course to @SternLab which this analysis was also published in a paper i collaborated with. docs.google.com/spreadsheets/d…
shay fleishon 🧬@shay_fleishon

I am posting an update here to the table of suspected chronic patients. I am also bringing a few interesting cases that can teach us about sequencing, epidemiology, and the significance of the data. This virus still take long journeys. 1/9

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Pathoplexus
Pathoplexus@pathoplexus·
📢 We're excited to introduce Pathoplexus, a specialized sequence database for human viral pathogens! 🌍 🧬 Launching with 4 viruses, Pathoplexus.org combines modern open-source software with transparent governance to improve global pathogen sequence sharing. 1/14
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Emily Smith
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 aaap.memberclicks.net/assets/Positio…
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Dr. Angela Rasmussen
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.
Helen Branswell 🇨🇦@HelenBranswell

.@USDA continues to insist that the #H5N1 #birdflu outbreak in cows can be stopped. Serious question: How do you stop transmission when you don't know where the virus is? statnews.com/2024/07/16/bir…

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Emily Smith
Emily Smith@EmilyAnne_Smith·
@RajlabN I’m glad to see more sequencing and data sharing of H5N1 from wild birds!
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Raj Rajnarayanan
Raj Rajnarayanan@RajlabN·
#H5N1 Updates 07/09/2024 More WGS sequences were uploaded to NCBI from @USDA #NVSL Total Sequences: 1216 (+162) These sequences have proper metadata (collection dates/geo location information). Source: ncbi.nlm.nih.gov/sra/ (search for WGS of H5N1) 1/n
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Josette Schoenmakers
Josette Schoenmakers@JosetteSchoenma·
@EmilyAnne_Smith @RyderRahil @nzm8qs @CorneliusRoemer I am still curious to see the GitHub issues for the 4 novel recombinants, if there are any. And do I understand correctly that not all available Californian sequenced samples van be found on GISAID? If so, is there a specific reason why?
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Keşfet

@CIDRAP @RajlabN @0bFuSc8 @jbloom_lab @CDCgov @shay_fleishon @AngieSHinrichs @SternLab