retro

A retrospective analysis of the COVID-19 pandemic and the modeling tools used throughout.

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Input Data

Most raw data used in this investigation is in the data/raw/ directory. This data has been culled and processed and formatted into data tables to be used for analysis. These tables are in the data/processed/ directory. Historical PyR0 and BVAS data exist in a different github repository, sars-cov2-modeling. Most of the raw data is publicly available at these sources:

• PyR0 historical results: sars-cov2-modeling github
• BVAS historical results: sars-cov2-modeling github
• Bloom fitness per mutation: SARS2-mut-fitness github
• Bloom DMS per mutation from DMS Paper: github
• EVEscape mutation effects (with some DMS): EVEscape paper Supplementary Table 6
• EVEscape strain effects: --Private repository at HMS--
  • /n/groups/marks/projects/CEPI/data/________/2023-10-28/all_seqs_EVEscape_scores.csv We also consider data from our own experiments. Through analysis of neutralization and infectivity analyses, we have regressed single-mutation effects on neutralization and infectivity of virus. This analysis is on github, and the data used here is at:
• data/processed/infectivity_mutation_effects.csv
• data/procedded/neutralization_mutation_effects_across_pools.csv
• data/procedded/neutralization_mutation_effects_within_pools.csv