The prevalence was assessed based on all samples in GISAID (downloaded on April 29, 2021) for a particular country based on PANGO lineage classification provided in GISAID metadata. Phylogenetic trees were built using Augur v. The samples shown in the phylogenetic trees were selected from GISAID database to cover significant lineages of interest (B.1.258 ∆H69/∆V70 variant in different countries and its outgroups and lineages containing ∆H69/∆V70 mutation and their outgroups).
Collection dates near to the important branching points are shown. This variant was particularly common in several European countries including the Czech Republic and Slovakia but has been quickly replaced by B.1.1.7 early in 2021.Ī Points of recurrent emergence of the ∆H69/∆V70 mutation. Phylogenetic analysis shows that the early sublineage of B.1.258 acquired the N439K substitution in the receptor-binding domain (RBD) of the Spike protein and, later on, also the deletion ∆H69/∆V70 in the Spike N-terminal domain (NTD). Sequencing of these samples revealed that although in some cases the samples were indeed confirmed as B.1.1.7, a substantial fraction of samples contained another ∆H69/∆V70 carrying mutant belonging to the lineage B.1.258, which has been circulating in Central Europe since August 2020, long before the import of B.1.1.7. We analyzed SARS-CoV-2 samples collected from various regions of Slovakia between November and December 2020 that were presumed to contain B.1.1.7 variant due to drop-out of the Spike gene target in an RT-qPCR test caused by this deletion.
SARS-CoV-2 mutants carrying the ∆H69/∆V70 deletion in the amino-terminal domain of the Spike protein emerged independently in at least six lineages of the virus (namely, B.1.1.7, B.1.1.298, B.1.160, B.1.177, B.1.258, B.1.375).
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