New: UK Health Security Agency published rapid analysis of BA.2.86 outbreak in a care home in Eurosurveillance Key messages: - 29/33 had Sanofi vaccine and initial Vaccine Effectiveness showed evidence of limited VE against infection 4 months post-vaccination eurosurveillance.org/content/10.280…

I am a researcher studying viruses. I have contributed to the sequencing of more than a million genomes deposited in the GISAID database. Last week I found that my access to bulk downloads from GISAID had been cut off without cause or explanation. [1/3]

Github copilot warned me that it had suggested some code that matched public code with unknown license. Turns out this was my own code 😇

Based on their prevalence and rate of growth, we've designated 3 new Nextstrain clades from Pango Network News lineages: 23G (XBB.1.5.70) 23H (HK.3) 23I (BA.2.86) 1/9

Here is my brief analysis of Dec-28-2019 SARSCoV2 submission to Genbank. This analysis supports my conclusion to WSJ (wsj.com/politics/natio…) that this submission does not tell origin of virus, but does show sequence known to Chinese Academy of Sciences weeks before released

Big thank you to whoever introduced the kwarg "delete" in tempfile.TemporaryDirectroy in Python 3.12! Just discovered it in the docs when I was looking for exactly this feature. Intellisense wasn't showing it as my env was using Python 3.11. Great reason to upgrade.

Ever wondered how fast accessory genome dynamics of bacteria really is? In a new preprint we (Marco Molari, Liam Shaw) explore how rapidly E coli picks up genes horizontally, breaks genome synteny, etc.. biorxiv.org/content/10.110… For a thread by Marco see mstdn.science/@mrcmlr/112772…

Uh oh GitHub

📢 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

One of the reasons I've been quiet on Twitter for a few months is because I've been working on something big - something I'm really happy to share now! Pathoplexus.org A new, open-source database for pathogen sequence sharing. 👐🧬🌎 1/12