Erik Aurell: SARS-CoV-2 genetics as seen from GISAID
GISAID (gisaid.org) is an initiative started a decade ago to host and share influenza data. During the COVID pandemic it has emerged as the main repository of SARS-CoV-2 genomic data. A an example, as of the time of writing this abstract (October 8, 2021), GISAID holds 4,185,387 SARS-CoV-2 submissions, many of them full-length genomes of this virus.
I will discuss some simple data analysis that can be done with this data, and some less simple and more speculative investigations. The simple part is straight-forward time series analysis of mutations listed for the variants now known as "alpha", "beta" and "delta" (UK, South Africa and India). From such an analysis one can, for instance, see that not all mutations listed initially could actually have been part of one variant growing as one clone.
The speculative part concerns analysis of covariation of pairs of mutations, and what such an analysis can tell us about SARS-CoV-2 biology.
The talk is based on joint work with Hong-Li Zeng, Vito Dichio, Edwin Rodríguez Horta, Kaisa Thorell and Rickard Norden (2020 and 2021).
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