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

Objectives: Surveillance of severe acute respiratory syndrome coronavirus 2 (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. Methods: SARS-CoV-2 sequences obtained from human nasopharyngeal samples by Illumina nextgeneration sequencing were analysed using NexraADE and an in-house PYTHON script and were compared using BLASTn to the GISAID database. Phylogeny was investigated using the IQ-TREE software. Results: We identified that SARS-CoV-2 genomes from four patients diagnosed in our institute harboured a new set of amino acid substitutions including LI8F, L452R, N501Y, A653V, H655Y, D796Y, G1219V +/- Q677H. These spike N501Y genomes are the first of Nextstrain Glade 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 individuals and in 2021 in 38 individuals. The 89 sequences obtained in our institute or other laboratories originated from the Comoros archipelago, western European countries (mostly metropolitan France), Turkey and Nigeria. Conclusion: These findings warrant further studies to investigate the spread, epidemiological and clinical features, and sensitivity to immune responses of this variant. (C) 2021 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Automated summary

Genomic surveillance of SARS-CoV-2 led to the identification of a new spike 501Y variant, with amino acid substitutions found in genomes from patients diagnosed in early 2021. Further investigation into the spread, epidemiology, and clinical impact of this variant is warranted.