Brona Brejova, Kristina Borsova, Viktoria Hodorova, Viktoria Cabanova, Lenka Reizigova, Evan D. Paul, Pavol Cekan, Boris Klempa, Jozef Nosek, Tomas Vinar. A SARS-CoV-2 mutant from B.1.258 lineage with H69/V70 deletion in the Spike protein circulating in Central Europe in the fall 2020. Virus genes, 2021.
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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). 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. 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. 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 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.