JHH influenza surveillance, side by side with Nextstrain's global builds

Compare clade, subclade and genotype frequencies in the Johns Hopkins Hospital network's public Nextstrain builds with the Nextstrain seasonal-flu builds, for A/H1N1pdm, A/H3N2 and B/Victoria.

Open the analysis → Have access to private builds? Run it on your computer

Runs entirely in your browser. Data loads live from nextstrain.org when you open it.

Local JHH public builds

Builds the Pekosz Lab has published in the PekoszLab-Public Nextstrain group.

Global Nextstrain seasonal-flu

The seasonal-flu builds, from 6 months to 12 years, HA and NA.

What you can do

Overlay or stack the two over the same timepoints, see the difference in percentage points, filter either or both datasets, and download figures and tables.

Relative frequencies only. Frequencies displayed in this dashboard represent taxa present in the supplied JHH local phylogeny builds and supplied Nextstrain seasonal-flu surveillance builds. They do not necessarily represent true circulating prevalence, complete regional prevalence, or all influenza sequences available in GISAID. The Nextstrain seasonal-flu builds are downsampled by their own pipeline; JHH builds include every sequence in the build.

Private builds

This website only ever reads public datasets. It never contacts the lab's private Nextstrain group, and it has no login. Lab members with access to the private builds can run the same app on their own computer, where the data stays.

Data and acknowledgements

Builds are produced with Nextstrain. The seasonal-flu builds use sequences shared via the GISAID Initiative; we gratefully acknowledge the authors and the originating and submitting laboratories of the genetic sequences and metadata. JHH sequences are generated by the Johns Hopkins Hospital network for JH-CEIRR. See each build on nextstrain.org for its full acknowledgements.