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. Author manuscript; available in PMC: 2024 Dec 14.
Published in final edited form as: Cell. 2024 Oct 8;187(25):7196–7213.e26. doi: 10.1016/j.cell.2024.09.026

Key resources table.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
FITC-conjugated chicken anti-Myc Immunology Consultants Laboratory, Inc. Cat# CMYC-45F
PE-conjugated goat anti-human IgG Jackson ImmunoResearch 109–115–098
Goat anti-mouse StarBright Blue 700 Bio-Rad Laboratories 12004159
Mouse anti-V5 tag Bio-Rad Laboratories MCA1360GA
Anti-AviTag polyclonal antibody GenScript A00674–40
S2V29 (S2V29-v1.2) IgG1m17-LS This paper N/A
VIR-7229 IgG1m17-LS This paper N/A
S2X259 IgG1m3-LS Tortorici, et al. 202121 N/A
SA55 IgG1m17-LS Cao, et al. 202242 N/A
VYD222 IgG1m3-LA Walker, et al. 202416 N/A
S309 IgG1m17-LS Pinto, et al. 202015 N/A
S2K146 IgG1m17-LS Park, et al. 202233 N/A
Omi-42 IgG1m17-YTE Nutalai, et al. 202227 N/A
VIR-7229 with Syrian hamster IgG2 Fc This paper N/A
Bacterial and virus strains
SARS-CoV-2 (Wild-type); hCoV-19/USA-WA1/2020 BEI Resources NR-52281
SARS-CoV-2 Delta (B.1.617.2); hCoV-19/USA/PHC658/2021 BEI Resources NR-55611
SARS-CoV-2 BA.1; hCoV-19/USA/MDHP20874/2021 BEI Resources NR-56461
SARS-CoV-2 BA.2.3; hCoV-19/USA/MDHP24556/2022 BEI Resources NRS-56511
SARS-CoV-2 BA.5; hCoV-19/USA/COR-22–063113/2022 BEI Resources NRS-58616
SARS-CoV-2 XBB.1.5; hCoV-19/USA/MD-HP40900/2022 BEI Resources NR-59104
SARS-CoV-2 XBB.1.16; hCoV-19/USA/CA-Stanford-139_S23/2023 BEI Resources NR-59442
SARS-CoV-2 EG.5.1; hCoV-19/USA/MD-HP47946/2023 BEI Resources NR-59576
SARS-CoV-2 FL.1.5.1; hCoV-19/USA/CA-AK001/2023 BEI Resources NR-59686
SARS-CoV-2 JN.1; hCoV-19/USA/NY/PV96109/2023 BEI Resources NR-59694
rVSV-spike-Wuhan-Hu-1; 21 amino acids deleted from spike C-terminus Case, et al. 202072 NCBI YP_009724390.1
rVSV-spike-XBB.1.5; C-terminal 19 amino acids deleted VectorBuilder N/A
rVSV-spike-EG.5; C-terminal 19 amino acids deleted VectorBuilder N/A
rVSV-spike-XBB.1.5.70; C-terminal 19 amino acids deleted VectorBuilder N/A
Biological samples
ExpiFectamine 293 Transfection Kit Gibco A14526
ExpiFectamine CHO Transfection Kit ThermoFisher Scientific 15627878
BirA biotin-protein ligase bulk reaction kit Avidity N/A
Chemicals, peptides, and recombinant proteins
Kifunensine Cayman Chemical NC9744221
Endo H New England Biolabs P0702L
PE-streptavidin Jackson ImmunoResearch 016–110–084
Critical commercial assays
ADCC Reporter Bioassay Promega G7018 (V158)
FcγRIIa-H ADCP Bioassay Promega G9995 (FcγRIIa)
Deposited data
XBB.1.5 RBD - VIR 7229 - S309 This paper PDB ID 9AU1
BQ.1.1 RBD - S2V29 - S2H97 This paper PDB ID 8S6M
EG.5 RBD - VIR 7229 - S2H97 This paper PDB ID 9ATM
BA.2.86 S:VIR-7229 (Local refinement) This paper PDB ID 9ASD, EMD-43813
BA.2.86 S:VIR-7229 (Global refinement) This paper PDB ID 9AU2, EM-43842
Illumina sequencing: barcode counts for pan-sarbecovirus yeast-display binding assay This paper NCBI SRA, BioProject PRJNA714677, BioSample SAMN41715061
Illumina sequencing: barcode counts for DMS mAb-escape yeast-display assay This paper NCBI SRA, BioProject PRJNA770094, BioSample SAMN41694243
Experimental models: Cell lines
HEK293T cells ATCC Cat# CRL-11268
Expi293F cells ThermoFisher Scientific A14527
ExpiCHO cells ThermoFisher Scientific A29127
Lenti-X 293T cells Takara 632180
Vero E6 cells ATCC CRL-1586
Vero-TMPRSS2 cells Lempp, et al. 2021 61 N/A
Experimental models: Organisms/strains
Saccharomyces cerevisiae strain AWY101 Wentz and Shusta 200775 N/A
Saccharomyces cerevisiae strain EBY100 ATCC MYA-4941
Male golden Syrian hamsters Janvier Laboratories Mesocricetus auratus; RjHan:AURA
Recombinant DNA
Yeast-display deep mutational scanning plasmid library, Wuhan-Hu-1 Starr et al. 202279 Addgene Cat# 1000000182
Yeast-display deep mutational scanning plasmid library, BA.2 Starr et al. 202253 Addgene Cat# 1000000188
Yeast-display deep mutational scanning plasmid library, BQ.1.1 Taylor and Starr 202360 Addgene Cat# 1000000231
Yeast-display deep mutational scanning plasmid library, XBB.1.5 Taylor and Starr 202360 Addgene Cat# 1000000232
Yeast-display deep mutational scanning plasmid library, EG.5 This paper Addgene Cat# pending
Yeast-display deep mutational scanning plasmid library, BA.2.86 This paper Addgene Cat# pending
Plasmids encoding amino acid positions 328–531 of SARS-CoV-2 Wuhan spike (NCBI reference YP_009724390.1) and Omicron variant spike proteins; N-terminal signal peptide; C-terminal 8xHis-AviTag or thrombin-8xHis-AviTag This paper N/A
Plasmid encoding SARS-CoV-2 BA.2.86 (EPI_ISL_18097315, amino acids 1–1204) Hexapro spike ectodomain; C-terminal foldon-AviTag-8xHis This paper N/A
Plasmid encoding residues 19–615 of human ACE2 (Uniprot Q9BYF1); N-terminal signal peptide; C-terminal thrombin cleavage site-TwinStrep-10xHis-GGG-tag This paper N/A
Software and algorithms
Custom computational pipeline for yeast-display pan-sarbecovirus binding assay This paper https://github.com/tstarrlab/SARSr-CoV_mAb-breadth_S2V29/blob/main/results/summary/summary.md
Custom computational pipeline for yeast-display mAb-escape DMS assay This paper
Biacore Insight Software Cytiva 29310602
Cryosparc v4.4.0 Punjani et al., 201790 https://cryosparc.com
Relion v3.0 Zivanov et al., 201895 https://www3.mrc-lmb.cam.ac.uk/relion
Coot Emsley et al., 201083 https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
Phenix Liebschner et al., 201985 https://phenix-online.org/download/
XDS Kabsch, 201081 https://xds.mr.mpg.de/
ChimeraX Pettersen et al., 2004102 https://www.cgl.ucsf.edu/chimerax/
Prism 10 GraphPad Software https://www.graphpad.com/features
Scikit-learn Pedregosa et al., 201170 scikit-learn: machinelearning in Python—scikit-learn 1.5.0documentation
Python version 3.10 Python software foundation www.python.org