https://github.com/cbg-ethz/covvfit

Fitness estimates of SARS-CoV-2 variants
https://github.com/cbg-ethz/covvfit

epidemiology fitness-landscape forecasting-models sars-cov-2 statistical-modeling virology wastewater-based-epidemiology wastewater-surveillance

Last synced: 10 months ago
JSON representation

Fitness estimates of SARS-CoV-2 variants

• Host: GitHub
• URL: https://github.com/cbg-ethz/covvfit
• Owner: cbg-ethz
• License: mit
• Created: 2023-10-27T12:35:10.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2025-08-01T05:31:48.000Z (11 months ago)
• Last Synced: 2025-08-17T04:37:34.229Z (10 months ago)
• Topics: epidemiology, fitness-landscape, forecasting-models, sars-cov-2, statistical-modeling, virology, wastewater-based-epidemiology, wastewater-surveillance
• Language: Python
• Homepage: https://cbg-ethz.github.io/covvfit/
• Size: 903 KB
• Stars: 2
• Watchers: 5
• Forks: 0
• Open Issues: 10
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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# covvfit

![Covvfit demonstration](docs/static/infer-output-figure.jpg)

Fitness estimates of SARS-CoV-2 variants from variant abundance data.

  - **Documentation:** [https://cbg-ethz.github.io/covvfit](https://cbg-ethz.github.io/covvfit)

  - **Source code:** [https://github.com/cbg-ethz/covvfit](https://github.com/cbg-ethz/covvfit)

  - **Bug reports:** [https://github.com/cbg-ethz/covvfit/issues](https://github.com/cbg-ethz/covvfit/issues)

## Installation and usage

*Covvfit* can be installed from the Python Package Index:

```bash

$ pip install covvfit

```

For an example how to analyze the data see [this tutorial](https://cbg-ethz.github.io/covvfit/cli/).

## References

This method accompanies our manuscript:

David Dreifuss, Paweł Piotr Czyż, Niko Beerenwinkel. *Learning and forecasting selection dynamics of SARS-CoV-2 variants from wastewater sequencing data using Covvfit*. medRxiv 2025.03.25.25324639; doi: [https://doi.org/10.1101/2025.03.25.25324639](https://doi.org/10.1101/2025.03.25.25324639)

```bibtex

@article{Dreifuss2025-Covvfit,

	author = {Dreifuss, David and Czy{\.z}, Pawe{\l} Piotr and Beerenwinkel, Niko},

	title = {Learning and forecasting selection dynamics of SARS-CoV-2 variants from wastewater sequencing data using Covvfit},

	elocation-id = {2025.03.25.25324639},

	year = {2025},

	doi = {10.1101/2025.03.25.25324639},

	publisher = {Cold Spring Harbor Laboratory Press},

	eprint = {https://www.medrxiv.org/content/early/2025/03/26/2025.03.25.25324639.full.pdf},

	journal = {medRxiv}

}

```

## See Also

  - [V-pipe](https://cbg-ethz.github.io/V-pipe/): a bioinformatics pipeline for viral sequencing data.

  - [cojac](https://github.com/cbg-ethz/cojac): command-line tools for the analysis of co-occurrence of mutations on amplicons.