1/ Updated #H5N1 timeline w/ events through May 2nd.

Biggest news:

I. Pasteurized milk is safe & no virus found in beef.
II. Municipal wastewater pos. for H5 (doesn't necessarily mean human cases, see below).
III. CDC expands guidance for farm workers.

Work w/ Brennan Klein & Moritz Kraemer

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 Posts.

Consensus genomes and metadata.

virological.org/t/note-about-a…

1/ Are you struggling to keep track of all the #H5N1 developments in the US?

Together w/ Brennan Klein & Moritz Kraemer, we started an open-access timeline of key events related to the outbreak.

As you can see, the situation is rapidly progressing, so we will keep updating.

USDA APHIS is tracking the cumulative number of cattle herds known to have high path H5N1. Moritz Kraemer made plot of each state's herd-based 'epi curve'.

General pattern: more and more herds affected.

But maybe leveling off in Texas (H/T Oliver Pybus )?

aphis.usda.gov/livestock-poul…

Here is a link to 239 consensus genome sequences, assembled by 👾 Karthik, from sequencing reads of 2.3.4.4b H5N1 influenza A virus from cattle and other species.

github.com/andersen-lab/a…

Florian Krammer 0bFuSc8 Dept. of Agriculture Raj Rajnarayanan Ryan Hisner Helen Branswell 🇨🇦 Rick Bright Dr Emma Hodcroft Louise Moncla Trevor Bedford Krutika Kuppalli, MD FIDSA Michael Mina Bloom Lab Caitlin Rivers Marion Koopmans, publications: https://pure.eur.nl the raw sequences are on SRA - very slowly going through them now but having the fastas public would save me a lot of time/effort....

I've spent a lot of time recently reflecting about diversity and privilege among epidemic modellers. I talked about it a Epidemics9 conference last year and I've now also summarised my thoughts in a written perspective: shorturl.at/efgtJ. Please share and discuss it!

Very insightful piece by Jon Cohen in Science Magazine News on the ongoing spread of bird flu in the US with specific mention of South-North movements of cattle at this time of year, coinciding with bird movements (see below)? science.org/content/articl…

I'm thrilled that my book, EUROPE WITHOUT BORDERS, will be out in January from Princeton University Press. It's a history of free movement, migration, and the contested status of borders in modern Europe. press.princeton.edu/books/hardcove…

The observed pattern of viral spread depends on the driving factors, but also on our detection capacity, which is heterogenous in space and time. This makes observations hard to decipher.

We tackled this challenge in the context of early SARS-CoV2 Alpha international invasion

Drivers and impact of the early silent invasion of SARS-CoV-2 Alpha now out Nature Communications

Great work led and coordinated by Chiara Poletto

nature.com/articles/s4146…