Visualizing how pathogens spread and change
Richard Neher
Biozentrum & SIB, University of Basel
slides at neherlab.org/202303_VizBi.html
Human seasonal influenza viruses
Positive tests for influenza in the USA by week
Data by the US CDC
Genome sequences record the spread of pathogens
in SARS-CoV-2 a new mutation accumulates about every 2 weeks
- Influenza viruses evolve to avoid human immunity
- Vaccines need frequent updates
Many data dimensions
- Phylogenetic tree -- hierarchical relatedness structure
- Genotype -- mutations and variants
- Dynamics and time
- Spatial distribution
- Phenotypes
Nextstrain.org
Hemagglutination Inhibition assays
Antigenic distance tables
- Long list of distances between sera and viruses
- Tables are sparse, only close by pairs
Integrating antigenic and molecular evolution
RN et al, PNAS, 2017
Integrating antigenic and molecular evolution
RN et al, PNAS, 2017
Integrating antigenic and molecular evolution
Jover Lee..., John Huddleston, 2023
Integrating antigenic and molecular evolution
Jover Lee..., John Huddleston, 2023
None of this works for millions of tips
Taxonium by Theo Sanderson
Pandemic scale trees by UShER
- phylogenetic tree of millions of samples grown through placement
- Fast search on this tree to explore the context of specific samples
- Extraction of the context and visualization in Nextstrain
Acknowledgments
Trevor Bedford and his lab -- terrific collaboration since 2014
especially James Hadfield, Emma Hodcroft, Ivan Aksamentov, Cornelius Roemer, Moira Zuber, and John Huddleston
Data we analyze are contributed by scientists from all over the world
Data are shared and curated by GISAID
