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Images and data for publication

This directory contains figures and tables output by the PyR0 model. These outputs are aggregated to weeks, PANGO lineages, and amino acid changes.

Figures and tables are generated by first running preprocessing and inference, then postprocessing with the following Jupyter notebooks: mutrans.ipynb , mutrans_gene.ipynb , mutrans_prediction.ipynb , mutrans_backtesting.ipynb .

Data tables

  • Mutation table is ranked by statistical significance. The "mean" field denotes the estimated effect on log growth rate of each mutation.
  • Lineage table is ranked by growth rate.

Manhattan plots

Manhattan plot of entire genome Manhattan plot of N gene Manhattan plot of S gene Manhattan plot of ORF1a gene Manhattan plot of ORF1b gene

Information density plots

ELBO of various genes ELBO of various NSPs

Volcano plot

Volcano plot of mutations

Strain characterization plots

Growth rate versus emergence date Growth rate versus case count Forecast Deep scanning

Cross validation plots

The following plots assess robustness via 2-fold crossvalidation, splitting data into Europe versus (World w/o Europe).

Lineage correlation Mutation correlation Lineage box plots Mutation box plots Mutation box plots Lineage prediction

Misc plots

Logistic distribution

Acknowledgements

The aggregated model outputs in this directory were generated from data inputs including GISAID records (https://gisaid.org), PANGO lineage classifications (https://cov-lineages.org), and case count time series from Johns-Hopkins University (https://github.com/CSSEGISandData/COVID-19).

We gratefully acknowledge all data contributors, i.e. the Authors and their Originating laboratories responsible for obtaining the specimens, and their Submitting laboratories for generating the genetic sequence and metadata and sharing via the GISAID initiative [1,2] on which this research is based. A total of 2,160,748 submissions are included in this study. A complete list of 2.1million accession numbers are available in accession_ids.txt.zip.

  1. GISAID Initiative and global contributors, EpiCoV(TM) human coronavirus 2019 database. GISAID (2020), (available at https://gisaid.org).
  2. S. Elbe, G. Buckland-Merrett, Data, disease and diplomacy: GISAID's innovative contribution to global health. Glob Chall. 1, 33-46 (2017).