Journal
VIRUS GENES
Volume 57, Issue 6, Pages 556-560Publisher
SPRINGER
DOI: 10.1007/s11262-021-01866-5
Keywords
SARS-CoV-2; B; 1; 1; 7; B; 1; 258; Variant; Spike; Deletion
Categories
Funding
- Slovak Research and Development Agency [APVV-18-0239, PPCOVID-20-0017, PP-COVID-20-0116]
- European Union's Horizon 2020 Research and Innovation program (EVA-GLOBAL Project) [871029]
- OPII project [ITMS2014, 313011ATL7]
- Scientific Grant Agency [VEGA 1/0463/20, VEGA 1/0458/18]
- European Union's Horizon 2020 Research and Innovation program (PANGAIA Project) [872539]
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SARS-CoV-2 mutants with H69/V70 deletion emerged in six lineages, including the B.1.1.7 variant. Samples from Slovakia showed a significant presence of the B.1.258 variant, which circulated in Central Europe before the arrival of B.1.1.7.
SARS-CoV-2 mutants carrying the increment H69/ increment 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 increment H69/ increment 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 increment H69/ increment 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.
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