Pitfalls of barcodes in the study of worldwide SARS-CoV-2 variation and phylodynamics.

ABSTRACT: Analysis of SARS-CoV-2 genome variation using a minimal number of selected informative sites conforming a genetic barcode presents several drawbacks. We show that purely mathematical procedures for site selection should be supervised by known phylogeny (i) to ensure that solid tree branches are represented instead of mutational hotspots with poor phylogeographic proprieties, and (ii) to avoid phylogenetic redundancy. We propose a procedure that prevents information redundancy in site selection by considering the cumulative informativeness of previously selected sites (as a proxy for phylogenetic-based criteria). This procedure demonstrates that, for short barcodes (e.g., 11 sites), there are thousands of informative site combinations that improve previous proposals. We also show that barco

SUBMITTER: Pardo-Seco J 

PROVIDER: S-EPMC7840454 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature