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

TL;DR

This study identifies and characterizes the B.1.258$ riangle$ SARS-CoV-2 variant circulating in Central Europe, highlighting its genetic features, prevalence, and potential impact on diagnostic testing and viral evolution.

Contribution

It reports the emergence and spread of the B.1.258$ riangle$ variant with specific deletions and mutations, distinct from the B.1.1.7 variant, and clarifies its phylogenetic history and regional prevalence.

Findings

B.1.258$ riangle$ has been circulating since August 2020 in Central Europe.

The variant carries the $ riangle$H69/$ riangle$V70 deletion and N439K mutation.

Routine PCR tests may misclassify B.1.258$ riangle$ as B.1.1.7.

Abstract

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$\Delta$.