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SARS-CoV-2 mutants carrying the $\Delta$H69/$\Delta$V70 deletion in the aminoterminal domain of the Spike protein emerged independently in at least sixlineages 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 adrop-out of the Spike gene target are incapable of distinguishing among theselineages and often lead to the false conclusion that clinical samples containthe B.1.1.7 variant, which recently emerged in the United Kingdom and isquickly spreading through the human population. We analyzed SARS-CoV-2 samplescollected from various regions of Slovakia between November and December 2020that were presumed to contain the B.1.1.7 variant due to traveling history ofthe virus carriers or their contacts. Sequencing of these isolates revealedthat although in some cases the samples were indeed confirmed as B.1.1.7, asubstantial fraction of isolates contained another $\Delta$H69/$\Delta$V70carrying mutant belonging to the lineage B.1.258, which has been circulating inCentral 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 theN439K substitution in the receptor binding domain (RBD) of the Spike proteinand, later on, also the deletion $\Delta$H69/$\Delta$V70 in the SpikeN-terminal domain (NTD). This variant is particularly common in severalEuropean countries including Czech Republic and Slovakia, and we propose toname it B.1.258$\Delta$.

B.1.258$\Delta$, a SARS-CoV-2 variant with $\Delta$H69/$\Delta$V70 in the Spike protein circulating in the Czech Republic and Slovakia