Spreading of a new SARS-CoV-2 N501Y spike variant in a new lineage.
Coronavirus disease 2019
Emergence
Epidemic
N501Y
Severe acute respiratory syndrome coronavirus 2
Spike
Variant
Journal
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases
ISSN: 1469-0691
Titre abrégé: Clin Microbiol Infect
Pays: England
ID NLM: 9516420
Informations de publication
Date de publication:
Sep 2021
Sep 2021
Historique:
received:
06
03
2021
revised:
31
03
2021
accepted:
01
05
2021
pubmed:
16
5
2021
medline:
14
9
2021
entrez:
15
5
2021
Statut:
ppublish
Résumé
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. SARS-CoV-2 sequences obtained from human nasopharyngeal samples by Illumina next-generation sequencing were analysed using Nextclade and an in-house Python script and were compared using BLASTn to the GISAID database. Phylogeny was investigated using the IQ-TREE software. We identified that SARS-CoV-2 genomes from four patients diagnosed in our institute harboured 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 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. These findings warrant further studies to investigate the spread, epidemiological and clinical features, and sensitivity to immune responses of this variant.
Identifiants
pubmed: 33991677
pii: S1198-743X(21)00226-3
doi: 10.1016/j.cmi.2021.05.006
pmc: PMC8114812
pii:
doi:
Substances chimiques
Spike Glycoprotein, Coronavirus
0
spike protein, SARS-CoV-2
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1352.e1-1352.e5Informations de copyright
Copyright © 2021 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.
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