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| Status |
Public on Sep 30, 2021 |
| Title |
SARS-CoV-2 spike P681R mutation, a hallmark of the Delta variant, enhances viral fusogenicity and pathogenicity |
| Organism |
Severe acute respiratory syndrome coronavirus 2 |
| Experiment type |
Genome variation profiling by high throughput sequencing
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| Summary |
During the current SARS-CoV-2 pandemic, a variety of mutations have been accumulated in the viral genome, and currently, four variants of concerns (VOCs) are considered as the hazardous SARS-CoV-2 variants to the human society. The newly emerging VOC, the B.1.617.2/Delta variant, closely associates with a huge COVID-19 surge in India in Spring 2021. However, its virological property remains unclear. Here, we show that the B.1.617.2/Delta variant is highly fusogenic, and notably, more pathogenic than prototypic SARS-CoV-2 in infected hamsters. The P681R mutation in the spike protein, which is highly conserved in this lineage, facilitates the spike protein cleavage and enhances viral fusogenicity. Moreover, we demonstrate that the P681R-bearing virus exhibits higher pathogenicity than the parental virus. Our data suggest that the P681R mutation is a hallmark that characterizes the virological phenotype of the B.1.617.2/Delta variant and is closely associated with enhanced pathogenicity.
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| Overall design |
To investigate the virological property of the B.1.617.2/Delta variant, the following recombinant viruses were generated by circular polymerase extension reaction (CPER) [Torii et al., Cell Rep., 2021; PMID: 33838744]: (i) WK-521 strain (GISAID ID: EPI_ISL_408667) with D614G mutation, (ii) WK-521 with D614G/P681R, (iii) GFP-inserted WK-521 with D614G, and (iv) GFP-inserted WK-521 with D614G/P681R. Regarding the recombinant viruses above and clinical isolates [a B.1.617.2/Delta isolate (EPI_ISL_2378732) and a D614G-bearing B.1.1 isolate (EPI_ISL_479681)], the viral supernatant stock (referred to as working virus) was prepared as follows: 100 μl of the seed virus was inoculated into VeroE6/TMPRSS2 cells (5,000,000 cells in a T-75 flask). At one hour after infection, the culture medium was replaced with Dulbecco’s modified Eagle’s medium (low glucose) (Wako, Cat# 041-29775) containing 2% FBS and 1% PS; at 2-3 days postinfection, the culture medium was harvested and centrifuged, and the supernatants were collected as the working virus. The genome sequences of the working viruses were verified using a viral RNA-sequencing analysis. Viral RNA was extracted using QIAamp viral RNA mini kit (Qiagen, Cat# 52906). The sequencing library for total RNA-sequencing was prepared using NEB Next Ultra RNA Library Prep Kit for Illumina (New England Biolabs, MA, Cat# E7530). Paired-end, 150-bp sequencing was performed using MiSeq (Illumina, San Diego, CA) with MiSeq Reagent Kit v3 (Illumina, Cat# MS-102-3001).
contributor: The Genotype to Phenotype Japan (G2P-Japan) Consortium
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| Contributor(s) |
Sato K |
| Citation(s) |
34823256 |
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| Submission date |
Aug 25, 2021 |
| Last update date |
Jan 11, 2022 |
| Contact name |
Kei Sato |
| E-mail(s) |
su9ark@gmail.com
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| Phone |
81364092212
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| Organization name |
The Institute of Medical Science, The University of Tokyo
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| Department |
Department of Microbiology and Immunology
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| Lab |
Division of Systems Virology
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| Street address |
4-6-1 Shiroganedai
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| City |
Minato-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
1088639 |
| Country |
Japan |
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| Platforms (1) |
| GPL28866 |
Illumina MiSeq (Severe acute respiratory syndrome coronavirus 2) |
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| Samples (6)
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| GSM5535846 |
Viral genomic RNA sequencing of a D614G-bearing B.1.1 isolate |
| GSM5535847 |
Viral genomic RNA sequencing of a B.1.617.2/Delta isolate |
| GSM5535848 |
Viral genomic RNA sequencing of a recombinant virus: WK-521 with D614G |
| GSM5535849 |
Viral genomic RNA sequencing of a recombinant virus: WK-521with D614G/P681R |
| GSM5535850 |
Viral genomic RNA sequencing of a recombinant virus: GFP-inserted WK-521 with D614G |
| GSM5535851 |
Viral genomic RNA sequencing of a recombinant virus: GFP-inserted WK-521with D614G/P681R |
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| Relations |
| BioProject |
PRJNA757684 |
| SRA |
SRP334053 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE182738_RAW.tar |
10.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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