Spreading of a new SARS-CoV-2 N501Y spike variant in a new lineage

Abstract

\n Objectives\n Our surveillance of the SARS-CoV-2 genomic epidemiology led us to detect several variants since summer 2020. We report the recent spread of a new SARS-CoV-2 spike 501Y variant.\n \n Methods\n SARS-CoV-2 sequences obtained from human nasopharyngeal samples by Illumina next-generation sequencing were analyzed using Nextclade and an in-house Python script and compared using BLASTn to the GISAID database. Phylogeny was performed using the IQ-TREE software.\n \n Results\n We identified that SARS-CoV-2 genomes from four patients diagnosed in our institute harbored a new set of amino acid substitutions including L18F;L452R;N501Y;A653V;H655Y;D796Y;G1219V±Q677H. These spike N501Y genomes are the first of Nextstrain clade 19B. We obtained partial spike gene sequences of this genotype for an additional 43 patients. All patients infected with this genotype were diagnosed since mid-January 2021. We detected 42 other genomes of this genotype in GISAID, which were obtained from samples collected in December 2020 in four cases and in 2021 in 38 cases. The 89 sequences obtained in our institute or other laboratories originated from the Comoros archipelago, Western European countries (mostly metropolitan France), Turkey and Nigeria.\n \n Conclusion\n These findings warrant further studies to investigate the spread, epidemiological and clinical features, and sensitivity to immune responses of this variant.\n