Rational identification of potent and broad sarbecovirus-neutralizing antibody cocktails from SARS convalescents

. 2022 Dec 1;41(12):111845. doi: 10.1016/j.celrep.2022.111845

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies

FITC anti-human CD19 antibody	BioLegend	Cat#392508; RRID: AB_2750099
FITC anti-human CD20 antibody	BioLegend	Cat#302304; RRID: AB_314252
Brilliant Violet 421™ anti-human CD27 antibody	BioLegend	Cat#302824; RRID: AB_11150782
PE/Cyanine7 anti-human IgM antibody	BioLegend	Cat#314532; RRID: AB_2566485
FITC-conjugated chicken anti-cMyc antibody	Immunology Consultants Laboratory, Inc.	Cat#CMYC-45F
BD series SARS-CoV-2 RBD antibodies	This study	N/A

Bacterial and virus strains

SARS-CoV-2 Wuhan-Hu-1 (SARS-CoV-2/human/CHN/CN1/2020)	This study	MT407649
SARS-CoV-2 Omicron BA.1 (SARS-CoV-2/human/CHN/Omicron-1/2021)	This study	OM095411
SARS-CoV-2 Omicron BA.5 (SARS-CoV-2/human/CHN/GD-5/2022)	This study	OP678016
DH10Bac E. coli	Invitrogen	Cat#10359-016

Cell lines

Saccharomyces cerevisiae strain EBY100	ATCC	MYA-4941
293T	ATCC	CRL-3216
HEK293F	ThermoFisher	Cat#R79007
Huh-7	JCRB	Cat#0403
293T-hACE2	SinoBiological	N/A
Vero	ATCC	CCL-81
HEK293F (in CD293)	ThermoFisher	Cat#11625019
Sf21	Invitrogen	Cat#B821-01
High Five	Invitrogen	Cat#B855-02

Chemicals, peptides, and recombinant proteins

X-tremeGENE 9 DNA Transfection Reagent	Roche	Cat#19129300
Polyethylenimine	Polysciences	Cat#23966-2
DMEM	ThermoFisher	Cat#11965092
HEPES	ThermoFisher	Cat#15630080
Iodoacetamide	Sigma Aldrich	Cat#I1149
SMM 293-TI medium	Sino Biological	Cat#M293TI
SIM SF medium	Sino Biological	Cat#MSF1
SIM HF medium	Sino Biological	Cat#MHF1
PE-conjugated streptavidin	ThermoFisher	Cat#S866
3% Glutamine	Gibco	Cat#21051
199 culture medium	BasalMedia	Cat#X103A6
SARS-CoV-2 (BA.4/BA.5) Spike RBD Protein (His Tag)	Sino Biological	Cat#40592-V08H130
SARS-CoV-2 (WT) Spike RBD Protein (His Tag)	Sino Biological	Cat#40592-V08H

Critical commercial assays

MoFlo Astrios EQ Cell Sorter	Beckman Coulter	N/A
EasySep™ Human CD19 Positive Selection Kit II	BioLegend	Cat#392508
Chromium Next GEM Single Cell 5′ Library & Gel Bead Kit v1.1	10x Genomics	PN-1000165
Chromium Single Cell 5′ Library Construction Kit	10x Genomics	PN-1000020
Chromium Single Cell V(D)J Enrichment Kit, Human B Cell	10x Genomics	PN-1000016
Chromium Next GEM Chip G Single Cell Kit	10x Genomics	PN-1000120
NovaSeq 6000 S4 Reagent Kit v1.5	Illumina	Cat#20028312
NovaSeq XP 4-Lane Kit v1.5	Illumina	Cat#20043131
QIAamp Viral RNA Mini Kit	Qiagen	Cat#52904
PrimeScript RT reagent Kit with gDNA Eraser	TaKaRa	Cat#RR047B
PrimeSTAR GXL DNA Polymerase	TaKaRa	Cat#R050B
Superdex 200 Increase 10/300 GL	Cytiva	Cat#28990944
Superose 6 Increase 10/300 GL	Cytiva	Cat#29091596
Biacore 8K	Cytiva	N/A
Series S Sensor Chip Protein A	Cytiva	Cat#29127556
Series S Sensor Chip CM5	Cytiva	Cat#29149603
His Capture Kit	Cytiva	Cat#29234602

Recombinant DNA

pVSV-SARS-CoV-2-S (Delta)	This study	encoding eGFP gene and codon-optimized SARS-CoV-2 Delta spike gene (GISAID: EPI_ISL_1911250) in place of VSV G
Plasmids expressing T7 polymerase and N, P, M and L of VSV, pcDNA3.1	Li et al., 2020⁴²	N/A
SARS-CoV-2 Omicron/Delta S gene, residues 1-1208, 6P and furin cleavage mutation, T4 fibritin trimerization motif, 8xHisTag, pcDNA	This study	N/A
BD55-5514 Fab, pcDNA	This study	N/A
BD55-5840 Fab, pcDNA	This study	N/A
BD55-3546 Fab, pcDNA	This study	N/A
BD55-4637 Fab, pcDNA	This study	N/A
BD55-5549 Fab, pcDNA	This study	N/A

Deposited data

Local refinement of BD55-4637 Fab in complex of BA.1 RBD	This study	PDB ID 7WRJ, EMD-32728
Local refinement of BD55-3546 Fab in complex of Delta RBD	This study	PDB ID 7WRY, EMD-32737
Local refinement of SA55 and SA58 Fab in complex of BA.1 RBD	This study	PDB ID 7Y0W, EMD-33552
BD55-5549 Fab in complex of BA.1 RBD	This study	PDB ID 7Y0V

Software and algorithms

PyMOL (version 2.6.0a0)	Schrödinger, LLC.	https://pymol.org
dms_variants (version 0.8.9)	The Bloom lab	https://github.com/jbloomlab/dms_variants
ggplot2 (version 3.3.3)	Wickham, 2016⁵³	https://ggplot2.tidyverse.org
FlowJo™ (version 10.8)	BD Biosciences	https://www.flowjo.com
logomaker (version 0.8)	Tareen and Kinney, 2019⁵⁴	https://github.com/jbkinney/logomaker
hisat2 (version 2.2.1)	Kim et al., 2019⁵⁵	http://daehwankimlab.github.io/hisat2/
HKL2000	HKL Research	https://www.hkl-xray.com/
PHENIX	Liebschner et al., 2019⁵⁶	https://www.phenix-online.org/
COOT	Emsley et al., 2010⁵⁷	https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot
SerialEM software	Mastronarde, 2005⁵⁸	https://bio3d.colorado.edu/SerialEM
MotionCor2	Zheng et al., 2017⁵⁹	https://emcore.ucsf.edu/ucsf-software
RELION	Zivanov et al., 2018⁶⁰	https://www2.mrc-lmb.cam.ac.uk/relion
UCSF Chimera	Pettersen et al., 2004⁶¹	https://www.cgl.ucsf.edu/chimera
UCSF ChimeraX	Pettersen et al., 2021⁶²	https://www.cgl.ucsf.edu/chimerax
Biacore Insight Evaluation Software (version 4.0.8)	Cytiva	N/A