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| Status |
Public on Jan 07, 2022 |
| Title |
Preparation of the working viruses of B.1.1, Delta and Omicron SARS-CoV-2 |
| Organism |
Severe acute respiratory syndrome coronavirus 2 |
| Experiment type |
Genome variation profiling by high throughput sequencing
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| Summary |
To investigate the virological properties of SARS-CoV-2 variants, we amplified the clinical isolates of an early pandemic D614G-bearing isolate (B.1.1 lineage, strain TKYE610670; GISAID ID: EPI_ISL_479681), a Delta isolate (B.1.617.2 lineage, strain TKYTK1734; GISAID ID: EPI_ISL_2378732) and an Omicron isolate (BA.1 lineage, strain TY38-873; GISAID ID: EPI_ISL_7418017) and prepared the working viruses.
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| Overall design |
To investigate the virological properties of SARS-CoV-2 variants, we amplified the clinical isolates of an early pandemic D614G-bearing isolate (B.1.1 lineage, strain TKYE610670; GISAID ID: EPI_ISL_479681), a Delta isolate (B.1.617.2 lineage, strain TKYTK1734; GISAID ID: EPI_ISL_2378732) and an Omicron isolate (BA.1 lineage, strain TY38-873; GISAID ID: EPI_ISL_7418017) using VeroE6/TMPRSS2 cells and prepared the working viruses. At 3 days postinfection, the culture media were 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, 76-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) |
35104835 |
| Submission date |
Dec 22, 2021 |
| Last update date |
Mar 25, 2022 |
| Contact name |
Kei Sato |
| E-mail(s) |
su9ark@gmail.com
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| Phone |
81757514813
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| Organization name |
Kyoto University
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| Department |
Institute for Frontier Life and Medical Sciences
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| Lab |
Laboratory of Systems Virology
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| Street address |
53 Shogoinkawara-cho, Sakyo-ku
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| City |
Kyoto |
| State/province |
Kyoto |
| ZIP/Postal code |
6068507 |
| Country |
Japan |
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| Platforms (1) |
| GPL28866 |
Illumina MiSeq (Severe acute respiratory syndrome coronavirus 2) |
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| Samples (3) |
| GSM5747642 |
Viral genomic RNA sequencing of a D614G-bearing B.1.1 isolate, resequenced |
| GSM5747643 |
Viral genomic RNA sequencing of a B.1.617.2/Delta isolate, resequenced |
| GSM5747644 |
Viral genomic RNA sequencing of a B.1.1.529/Omicron isolate, resequenced |
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| Relations |
| BioProject |
PRJNA791622 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE192472_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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