B.1.258∆, a SARS-CoV-2 variant with ∆H69/∆V70 in the Spike protein circulating in the Czech Republic and Slovakia
We analyzed SARS-CoV-2 samples collected from various regions of Slovakia between November and December 2020 that were presumed to contain the B.1.1.7 variant due to traveling history of the virus carriers or their contacts. Sequencing of these isolates revealed that although in some cases the samples were indeed confirmed as B.1.1.7, a substantial fraction of isolates 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. 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). This variant is particularly common in several European countries including Czech Republic and Slovakia, and we propose to name it B.1.258∆.
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