  SARS-CoV-2 mutants carrying the $\Delta$H69/$\Delta$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). Routine RT-qPCR tests including TaqPath or similar assays based on a
drop-out of the Spike gene target are incapable of distinguishing among these
lineages and often lead to the false conclusion that clinical samples contain
the B.1.1.7 variant, which recently emerged in the United Kingdom and is
quickly spreading through the human population. 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 $\Delta$H69/$\Delta$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 $\Delta$H69/$\Delta$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$\Delta$.
