v1.0.0

Variant Hunter is here!

VariantHunter analyzes the frequencies of amino acid mutations of SARS-CoV-2 in order to observe interesting variant trends or identify novel emerging variants.

Features

VariantHunter supports two modes of analysis: Lineage Independent and Lineage Specific. Each mode allows to open several analysis sessions (managed in panels that can be expanded, collapsed, or deleted at the user's choice).

The underlying mechanism of both methodologies is the same: each amino acid mutation is analyzed for a time period of 4 weeks.
For each week, the frequency of the mutation (computed as "number of sequencing harboring the mutation"/"total number of sequences collected in that week") is considered; then, a linear model is fitted on the four data points.

The slope of the regression line represents how fast the mutation is growing (i.e., its percentage is increasing). Positive slopes indicate an increasing trend, while negative values of the slope indicate a decreasing trend.

Chi squared tests are computed to test the significance of the change of frequency of the mutation.

The main results of both analyses are summarized in a table of mutations, reporting their prevalence over the 4 weeks, their slope, and Chi squared tests p-values. In addition, different visualizations support the intuition of the observed trends of diffusion: a heatmap and various line-plots that represent prevalence or their odd ratios.