globaldothealth / covid19-variants-summary

This code summarises data from GISAID by epiweek. Outputs and analyses using these data are published in Gonçalves et al. eLife 2022;11:e80556. DOI: https://doi.org/10.7554/eLife.80556

COVID-19 variants summary

This code summarises data from GISAID by epiweek. Outputs and analyses using these data are published in Gonçalves et al. eLife 2022;11:e80556. DOI: https://doi.org/10.7554/eLife.80556

Requirements

Python 3.6 or later.

Python modules: pandas, epiweeks

To install the modules in a virtual environment:

python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt
python3 analysis.py  # run analysis

Data

Place GISAID metadata at gisaid/metadata.tsv

Output

All output files are in the output folder.

• weekly.csv: Main output file with weekly totals of VOC Omicron and Delta as well as other variants by country. We use the epiweeks package to calculate CDC epiweeks (starting on Sunday).

• completeness.csv: Completeness as percentage of fields which are not null, other than the Patient age field which is the percentage of fields which are of type float.

• gender.txt: The gender field in GISAID is particularly error-prone with many instances of ages and mis-spellings. This lists all the unique values in the Gender field by country.