New paper: Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

Zam Iqbal, at the University of Bath, led this epic study published today in Nature Methods where we assembled all SARS-CoV-2 genomes deposited in the European Nucleotide Archive before 2 March 2023. In total a staggering 4,395,655 samples were processed. Since SARS-CoV-2 was almost always sequenced using tiled amplicons (e.g. ARTICv3), he and his team wrote viridian which is a variant caller that identifies the amplicon scheme used and then uses that information to avoid making spurious calls. The resulting phylogenetic tree is much more consistent than other trees built from publicly-available consensus sequences. You can explore the huge phylogenetic tree in detail here.