Mutation frequency time series reveal complex mixtures of clones in the world-wide SARS-CoV-2 viral population

TL;DR

This study analyzes the mutation frequency time series of SARS-CoV-2 variants using nearly two million genomes, revealing complex mixtures of clones and diverse genetic characteristics within what are considered single variants.

Contribution

The paper introduces a large-scale analysis of SARS-CoV-2 mutation frequencies over time, uncovering the complex genetic diversity within variants.

Findings

Majority of alpha mutations rose in late 2020 and diverged in 2021.

Delta mutations showed similar temporal patterns to alpha.

Beta variant exhibited a complex pattern with some mutations rising and others remaining low.

Abstract

We compute the allele frequencies of the alpha (B.1.1.7), beta (B.1.351) and delta (B.167.2) variants of SARS-CoV-2 from almost two million genome sequences on the GISAID repository. We find that the frequencies of a majority of the defining mutations in alpha rose towards the end of 2020 but drifted apart during spring 2021, a similar pattern being followed by delta during summer of 2021. For beta we find a more complex scenario with frequencies of some mutations rising and some remaining close to zero. Our results point to that what is generally reported as single variants is in fact a collection of variants with different genetic characteristics. For all three variants we further find some alleles with a clearly deviating time series.