Growth of variants

[adamkucharski]

• Pipeline for GISAID (and other) databases, (multinomial) logistic growth models
• R package to analyze the growth advantage of new (SARS-CoV-2) variants from genomic surveillance data

WHO Collaboratory Hackathon Idea.

[adamkucharski]

This was used quite a lot for COVID so might be a good starting point: https://github.com/tomwenseleers/LineageExplorer

[calthaus]

The Gerstung Lab also has some material (albeit in Python):

• https://github.com/gerstung-lab/genomicsurveillance
• https://github.com/gerstung-lab/SARS-CoV-2-International

@lborcard and @malare from the University of Bern have worked on a Shiny app to track SARS-CoV-2 variants, which could be included in a package. @finlaycampbell might also be interested to contribute to such a package development.

[finlaycampbell]

Yes happy to be involved/kept in the loop with this! I did quite a lot of internal work on this but we never got round to publishing the code even though it is fairly well-documented/packaged. I used the outbreakinfo package to pull GISAID data, though also had the option to import the GISAID data from a locally downloaded file.

[calthaus]

@jabacker from RIVM has also worked on this and could give valuable input. I will try to set up a meeting with all of us in the coming weeks to discuss how we move forward.

[adamkucharski]

Oliver Johnson at Bristol has also been doing regular updates on COVID variants using some MLE-based approaches (e.g. https://bristoliver.substack.com/p/covid-graphs-update) so expect he'll have some useful input on common obstacles/bottlenecks in producing quick early insights – he said he'd be interested in being looped in.

[adamkucharski]

Talking with Moritz Kraemer, he'd also be interested in discussing – they're working on pipelines for genomic analysis with GRAPEVNE so could be an opportunity to build module here.