Swiss national Sars-CoV-2 genomic surveillance program: Plots and Tables

Figure 1: Total number of sequences produced per the Swiss genomic SARS-CoV-2 surveillance program

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Figure 2: Total number of sequences per calendar week per surveillance region

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Figure 3: Variant share per calendar week in Switzerland

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Figure 4: Variant share in the most recent 4 complete calendar weeks by surveillance region

Description

Command line program to create plots and tables for the monthly report of the Swiss national Sars-CoV-2 genomic surveillance program.

Sequencing data is obtained from covSpectrum's public API (for docs see https://github.com/cevo-public/cov-spectrum-docs/blob/develop/API.md)

Data is merged and binned by calendar week (beginning on Mondays). Data from cantons is aggregated to 6 Swiss Sentinella Surveillance Region:

Region 0: All of Switzerland (CH)
Region I: Genève (GE), Vaud (VD), Valais (VS) and Neuchâtel (NE)
Region II: Bern (BE), Fribourg (FR) and Jura (JU)
Region III: Basel-Stadt (BS), Basel-Land (BL), Aargau (AG) and Solothurn (SO)
Region IV: Luzern (LU), Zug (ZG), Nidwalden (NW), Obwalden (OW), Uri (UR), Schwyz (SZ) and Glarus (GL)
Region V: Zürich (ZH), Schaffhausen (SH), Thurgau (TG), St-Gallen (SG), Appenzell-Innerhoden (AI) and Appenzell-Ausserhoden (AR)
Region VI: Graubünden (GR), Ticino (TI) 

Usage

usage: main.py [-h] [-d] [-p] [-t] [-s START_DATE] [-e END_DATE] [-o OUTPUT_DIR]

optional arguments:
  -h, --help            show this help message and exit
  -d, --download        download data, if unset, use stored data
  -p, --plot            create plots
  -t, --table           create tables
  -s START_DATE, --start-date START_DATE
                        start date - format YYYY-MM-DD
  -e END_DATE, --end-date END_DATE
                        end date - format YYYY-MM-DD
  -o OUTPUT_DIR, --output-dir OUTPUT_DIR
                        output sub-directory

Requirements (for precise versions see requirements.txt):

• pandas
• matplotlib
• requests

Do fresh data download as follows:

./main.py --download

Create plots for May in folder /plots/2021-05/ (plots are generated both in png and pdf formats in respective folders)

./main.py --plot --start-date 2021-04-01 --end-date 2021-06-07 --output-dir 2021-05 

Create table with all calendar weeks whose Monday occurs in May /tables/2021-05/:

./main.py --tables --start-date 2021-05-01 --end-date 2021-06-01 --output-dir 2021-05 

Maintenance

Variant definitions are in /scripts/variant_to_pango.py

Region definitions in /scripts/surveillance_region_map.py

Ground truth CSV definitions

All plots and tables are generated from a ground truth file placed in data/cases_seq_by_cw_region.csv that is generated by the program itself.

• reg: int for surveillance region, 0 stands for all of Switzerland
• date: Date of first day (= Monday) of respective calendar week
• Beta,...: Number of variants identified through sequencing
• Others: Any sequences that are not already accounted for in the named variant columns
• Sequences: Sum of all sequences
• Cases: Case count according to BAG dashboard