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Natural selection analysis from Sergei Pond's research group   (All Variation and Repeats tracks)

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 Common Variants  Common Variants implicated in data from Sergei Pond's research group   Schema 
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 Increasing frequency  Increasing frequency sites implicated in data from Sergei Pond's research group   Schema 
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 Intra host variants  Intra-host variants implicated in data from Sergei Pond's research group   Schema 
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 Multiple Clades  Sites implicated in multiple clades by Sergei Pond's research group   Schema 
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 Negative Selection  Sites of negative selection implicated in data from Sergei Pond's research group   Schema 
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 New  Sites implicated in data from Sergei Pond's research group   Schema 
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 Positive Selection  Sites of positive selection implicated in data from Sergei Pond's research group   Schema 
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 predicted CTL epitopes  Predicted CTL epitopes implicated in data from Sergei Pond's research group   Schema 
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 Selected in animals  Sites of selection in animals implicated in data from Sergei Pond's research group   Schema 
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 Selection Sites  Sites of selection implicated in data from Sergei Pond's research group   Schema 
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 Unexpected residues  Unexpected residues implicated in data from Sergei Pond's research group   Schema 
    


new Note: Released Aug. 28, 2020

Description

This track shows data from Pond et al, 2020 "Natural selection analysis of SARS-CoV-2/COVID-19"

The authors use several statistical techniques to identify selection sites of interest in SARS-CoV-2 data from GISAID. Each site receives points for eight different categories, explained below, and sites with the most points are ranked higher.

Display Conventions and Configuration

The gray to black color scale denotes increasing scores for selection sites where each site has the potential to receive one additional point for any of the eight following categories.

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 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"

Multiple Clades: "If a site belongs to this category, then at least two internal branches in the tree are inferred to be subject to positive selection, implying several selective events (not just a single introduction)"

Increasing frequency: "When a site belongs to this category, alternative amino-acids at this site has an increasing frequency trend (based on applying the Jonckheere-Terpstra test to 10-day intervals)"

Predicted CTL epitopes: "This site belongs to one or more CTL linear epitopes that are predicted to be recognized by one or more HLA alleles reported in Campbell et al"

Intra-host variants: "When a site belongs to this category, there is at least one deep sequencing dataset that shows the presence of intra-host variation at the same site at between 2 and 90%."

Unexpected residues: "When a site belongs to this category, there is at least one amino-acid present in more than one sequence that was not predicted to occur at this site based on the evolution of other betacoronaviruses. It might indicate evolutionary events that we have not observed in similar viruses before."

Selected in animals: "There is evidence of positive selection or differential selection acting on the bat/pangolin isolates closely related to the SARS-CoV-2 genome based on data from Boni et al"

New is any site that was recently detected as of June 30th, 2020.

Selection is any site at which positive or negative selection occurs.

For representation purposes scores (0-7) have been scaled to 500-1000.

Methods

The JSON used to generate the Genomic Coordinates of selection sites was parsed and the position, gene, site_in_gene, kind, score, and type fields were used to generate the resulting fields provided for each "kind" provided in the data.

References

Pond et al, 2020 "Natural selection analysis of SARS-CoV-2/COVID-19"

For questions, email nmauldin@ucsc. edu or jferna10@ucsc. edu.