A SARS-CoV-2 mutant from B.1.258 lineage with increment H69/ increment V70 deletion in the Spike protein circulating in Central Europe in the fall 2020

被引:27
作者
Brejova, Brona [1 ]
Borsova, Kristina [2 ,3 ]
Hodorova, Viktoria [4 ]
Cabanova, Viktoria [2 ]
Reizigova, Lenka [5 ,6 ]
Paul, Evan D. [7 ]
Cekan, Pavol [7 ]
Klempa, Boris [2 ]
Nosek, Jozef [4 ]
Vinar, Tomas [1 ]
机构
[1] Comenius Univ, Fac Math Phys & Informat, Bratislava 84248, Slovakia
[2] Slovak Acad Sci, Inst Virol, Biomed Res Ctr, Dubravska Cesta 9, Bratislava 84505, Slovakia
[3] Comenius Univ, Fac Nat Sci, Dept Microbiol & Virol, Ilkovicova 6, Bratislava 84215, Slovakia
[4] Comenius Univ, Fac Nat Sci, Dept Biochem, Ilkovicova 6, Bratislava 84215, Slovakia
[5] Reg Author Publ Hlth, Trencin, Slovakia
[6] Trnava Univ, Fac Healthcare & Social Work, Dept Lab Med, Trnava, Slovakia
[7] Comenius Univ Bratislava Sci Pk, MultiplexDX Sro, Ilkovicova 8, Bratislava 84104, Slovakia
基金
欧盟地平线“2020”;
关键词
SARS-CoV-2; B; 1; 7; 258; Variant; Spike; Deletion;
D O I
10.1007/s11262-021-01866-5
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
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.
引用
收藏
页码:556 / 560
页数:5
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