Postdoc @UCLA | PhD @scrippsresearch | https://xitter.cf/t.co/K5wjiCFNGw | 🐘@gk@mstdn.science
La Jolla
Joined April 2010
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👾 Karthik retweeted
Got milk virus genomes? (or any H5N1?) Throw them at usher.bio and see where they land in per-segment trees of tens of thousands of public Influenza A H5N1 sequences!
👾 Karthik retweeted
For a report on our analyses of #H5N1 in cattle, see
worobey bsky social
👾 Karthik retweeted
My colleagues and I have just posted a
"Note about availability of #H5N1 2.3.4.4b consensus sequences from cattle and other species" @virological_org.
Consensus genomes and metadata.
virological.org/t/note-about…
👾 Karthik retweeted
#GPUalgorithms achieve significant speedup in statistical #phylogenetics, exemplified by estimating West Nile virus introduction timing from 104 genomes using BEAGLE v4.0.0 in BEAST. [co-authored by EVBC members @LemeyLab @suchard_group] doi.org/10.1093/bioinformati…
👾 Karthik retweeted
In a @VanityFair story, @KatherineEban oddly misrepresented an investigation into @GISAID and Peter Bogner by @sciencecohen and me; suggested our story was a volley in the lab leak debate; and let Bogner dismiss it as a "hit piece." Here's our response. science.org/do/10.1126/scien…
👾 Karthik retweeted
My colleague @sciencecohen and I spent months investigating @GISAID and the mysterious man behind it, Peter Bogner. Here's what we found. science.org/content/article/…
Great to see these API connections!
Had a good week participating in the NCBI Beyond Phylogenies codeathon. One of the things our team achieved was to add links between tools used for viral phylogenetics
You can now:
- load @nextstrain trees in Taxonium
- export out NS subtrees
- get clade stats with @GenSpectrum
👾 Karthik retweeted
🧵for our latest preprint on the intrahost evolution of SARS-CoV-2 virus in an immunocompromised individual (60s) with a history of cancer chronically infected for at least 471 days (ongoing) with consistently replicating viruses at a high viral load. 1/n
medrxiv.org/content/10.1101/…
We've been working hard to enable quicker and easier ⚡️ access to simple but key SC2 variant statistics 📉📈 on @DiseaseOutbreak
Our R package now lets any user with @GISAID credentials to quickly access these stats for surveillance efforts 🔍 & complex downstream analyses 🤓
We've also described the technical details on outbreak.info in these preprints,
Genomic reports
medrxiv.org/content/10.1101/…
Research Library
biorxiv.org/content/10.1101/…
This was a big team effort only made possible by global 🗺️ sequencing efforts and the team at @GISAID!
In particular, I wanted to highlight @malkuzweny's work in building the R package. She has gone on to doing more exciting work as a PhD student in @TAlexPerkins's group!
👾 Karthik retweeted
we're deep into Omicron's reign. does that mean we definitely need an Omicron-specific vaccine?
it's complicated for at least three big reasons: timing, Omicron's weirdness, and the vagaries of virus evolution. 1/
theatlantic.com/health/archi…
👾 Karthik retweeted
We have just released two preprints on the origin of SARS-CoV-2:
1. "The Huanan market was the epicenter of SARS-CoV-2 emergence"
zenodo.org/record/6299116#.Y…
👾 Karthik retweeted
I wrote about what's next for the pandemic—the decisions we will *have* to make, if we are to bring COVID under control. 1/
theatlantic.com/science/arch…
👾 Karthik retweeted
(1/13) By the end of the Omicron wave, nearly all of us will have glimpsed spike in some form or another—injection, infection, both. I wrote about what that means... and why “widespread exposure” does not necessarily equate to “widespread protection.”
theatlantic.com/health/archi…
Data on outbreak.info @DiseaseOutbreak has been updated to include BA.1.1. As noted by many, the dynamics of the sub lineages within Omicron are changing.
Globally 🌍,
- BA.1.1 (BA.1 + S:346K), grew and seems to have plateaued.
- BA.2 📈
- BA.1 📉
In the meantime, the @DiseaseOutbreak team is working hard to keep everything up to date!