Preparation of the working viruses of B.1.1, Delta and Omicron SARS-CoV-2

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. 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