Sars cov 2 variant update:
In this week @corneliusroemer.bsky.social and XZ spotted a couple of lineages with very divergent spikes:

Silence will not shield scientists from the consequences of an increasingly hostile political landscape.

UK and other non-US scientists must act to support our US colleagues.

Here's what I think we should be doing...

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Detecting SARS-CoV-2 Cryptic Lineages using Publicly Available Whole Genome Wastewater Sequencing Data Beginning in early 2021, unique and highly divergent lineages of SARS-CoV-2 were sporadically found in wastewater sewersheds using a sequencing strategy focused on the most mutagenic region of SARS-Co...

I’m pleased to share that we FINALLY submitted our latest manuscript on SARS-CoV-2 cryptic lineages and what they tell us about the origins of COVID-19.
This was a ton of work.
medrxiv.org/cgi/content/...
1/

Map shows the location of wastewater sampling locations around the US. Most of the sites indicate low levels and are colored blue. However, there are a number of sites in CA with high levels and few other scattered sites around the US with medium/high levels and are colored in orange/red

1/ Influenza wastewater activity levels are currently low across the US, aside from conspicuous areas in CA where #H5N1 is spreading in dairy cows.

A deeper dive into the Wastewater Scan data paints a very concerning picture and should add to our sense of urgency.

Done

Note to journalists: important to communicate that the stated aim of GBD was to have a massive epidemic (immediately before vaccines became available), and also somehow keep it away from older population at higher risk (which would be about 25% of UK population if take age 60 as cutoff)

H5N1 is showing
1) stepwise mutation capabilities, but the direction of those is very diverging . So more than the subs rate i am worried about "innate" antigenic evolution capability
2) intra host saltation capability (like Tamiflu resistance mutation) despite very little diffused immuno pressure

The panzonootic H5N1 in the making is alarming

and yes, i am an alarmist

Because nobody seems to care

And that is alarming

proudly member of
#varianttrackinggroup

with
@siamosolocani.bsky.social

I’ve updated SARSCoV2 RBD antibody-escape calculator w new deep mutational scanning data of Yunlong Cao & Fanchong Jian.

My interpretation: antigenic evolution currently constrained by pleiotropic effects of mutations on RBD-ACE2 affinity, RBD up-down position & antibody neutralization