About CMVividly
I’m Damon May, a lead author of the July bioRxiv preprint “Immune signatures of common exposures through co-occurrence of T-cell receptors in tens of thousands of donors”. That work discovers the public T-cell responses to viruses, bacteria, etc., by finding groups of T-cell receptors (TCRs) that tend to occur in the same people. We call those TCR clusters ECOclusters. I wrote a pretty good backgrounder on this stuff for DIA Global Forum in 2025.
In July 2026, we made a major update to the preprint (v3). More samples, new methods, better ECOclusters. The preprint makes a dramatically updated “CMV ECOcluster” available as supplemental data. This group of TCRs represents humanity’s collective, public response to Cytomegalovirus, a chronic virus that dramatically reshapes the T-cell repertoire. More formally, the CMV ECOcluster defines a sensitive, specific and quantitatively useful biomarker of CMV infection (much more detail in the preprint).
Here, I’m doing public data exploration of the CMV ECOcluster to help the AIRR community and others make the best use of this new public resource. I’ll post updates when I have new analysis to share here and publicize them on my LinkedIn.
1 To reproduce these posts
Clone the CMVividly github repo and install python and uv.
From the repository root:
uv sync
uv run quarto renderOr, with a regular virtual environment:
python -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt
quarto render