This track shows data from Sergei Pond's research group, updated several
times between 2020 and 2022, with results published in 2022. The current
dataset is from February 2022 and is scheduled to be updated soon. Contact us
or Sergei if you believe that the data shown is too outdated for your analyses.
The authors use several statistical techniques to identify selection sites
of interest in SARS-CoV-2 data from GISAID.
Display Conventions and Configuration
This track has two subtracks:
Positive Selection: "On average along interior
tree branches, this site has a dN/dS>1 is accumulating non-synonymous changes (some
of which might have a functional impact, but most probably don't) faster
relative to synonymous changes than would be expected under neutral evolution."
Negative Selection: "On average along interior
tree branches, this site has a dN/dS<1, meaning that it is conserved, i.e.
non-synonymous changes might be selected against. Note that sites with no
changes (i.e. perfectly conserved sites) cannot be detected by dN/dS based methods"
The CSV used to generate the genomic coordinates of selection sites was parsed
and the position, gene, site_in_gene, score, and type fields were used to
generate the resulting fields provided for each site in the data.
Pond et al, 2020
"Natural selection analysis of SARS-CoV-2/COVID-19"
Pond et al, 2020
"Natural selection analysis of SARS-CoV-2/COVID-19, V2"
Martin DP, Lytras S, Lucaci AG, Maier W, Grüning B, Shank SD, Weaver S, MacLean OA, Orton RJ,
Lemey P et al.
Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That
Likely Impact Spike Function.
Mol Biol Evol. 2022 Apr 11;39(4).
PMID: 35325204; PMC: PMC9037384