Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response.
A549 Cells
Adolescent
Adult
Aged
Aged, 80 and over
Animals
Base Sequence
COVID-19
/ blood
Cell Line
Child
Child, Preschool
Chlorocebus aethiops
Female
Gene Deletion
Genomics
HEK293 Cells
Humans
Infant
Interferon Type I
/ blood
Interferon-beta
/ blood
Male
Middle Aged
Molecular Epidemiology
Reverse Genetics
SARS-CoV-2
/ genetics
Vero Cells
Viral Nonstructural Proteins
/ genetics
Young Adult
COVID-19
Nsp1
SARS-CoV-2
association
clinical phenotype
deletion
genetic variants
genomic epidemiology
interferon
reverse genetics
Journal
Cell host & microbe
ISSN: 1934-6069
Titre abrégé: Cell Host Microbe
Pays: United States
ID NLM: 101302316
Informations de publication
Date de publication:
10 03 2021
10 03 2021
Historique:
received:
21
12
2020
revised:
07
01
2021
accepted:
26
01
2021
pubmed:
7
2
2021
medline:
25
3
2021
entrez:
6
2
2021
Statut:
ppublish
Résumé
The SARS-CoV-2 virus, the causative agent of COVID-19, is undergoing constant mutation. Here, we utilized an integrative approach combining epidemiology, virus genome sequencing, clinical phenotyping, and experimental validation to locate mutations of clinical importance. We identified 35 recurrent variants, some of which are associated with clinical phenotypes related to severity. One variant, containing a deletion in the Nsp1-coding region (Δ500-532), was found in more than 20% of our sequenced samples and associates with higher RT-PCR cycle thresholds and lower serum IFN-β levels of infected patients. Deletion variants in this locus were found in 37 countries worldwide, and viruses isolated from clinical samples or engineered by reverse genetics with related deletions in Nsp1 also induce lower IFN-β responses in infected Calu-3 cells. Taken together, our virologic surveillance characterizes recurrent genetic diversity and identified mutations in Nsp1 of biological and clinical importance, which collectively may aid molecular diagnostics and drug design.
Identifiants
pubmed: 33548198
pii: S1931-3128(21)00045-7
doi: 10.1016/j.chom.2021.01.015
pmc: PMC7846228
pii:
doi:
Substances chimiques
Interferon Type I
0
NSP1 protein, SARS-CoV-2
0
Viral Nonstructural Proteins
0
Interferon-beta
77238-31-4
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
489-502.e8Informations de copyright
Copyright © 2021 Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of interests The authors declare no competing interests.