SARS-CoV-2 antibodies from children exhibit broad neutralization and belong to adult public clonotypes

. 2023 Nov 6;4(11):101267. doi: 10.1016/j.xcrm.2023.101267

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies

APC-Cy7 Mouse Anti-Human CD14	BD	Cat# 561709; RRID: AB_10893806
FITC Anti-Human CD3 (OKT3)	Tonbo Biosciences	Cat# 35–0037; RRID: AB_2621662
BV711 Mouse Anti-Human CD19	BD	Cat# 563036; RRID: AB_2737968
PE-Cy5 Mouse Anti-Human IgG	BD	Cat# 551497; RRID: AB_394220
Goat anti-human IgG antibody (peroxidase)	Jackson ImmunoResearch	Cat#109-035-088, RRID:AB_2337584
Anti-Mouse IgG HRP Conjugate	Promega	Cat#W4021
Monoclonal anti-influenza 3602-1707	Setliff et al.⁴³	N/A
Monoclonal anti-SARS-CoV-2 NTD 5317-9	Shiakolas et al.³⁷	N/A
Monoclonal anti-SARS-CoV-2 71281-3	This paper	GenBank: OR486977, OR486978
Monoclonal anti-SARS-CoV-2 71281-6	This paper	GenBank: OR486983, OR486984
Monoclonal anti-SARS-CoV-2 71281-20	This paper	GenBank: OR487011, OR487012
Monoclonal anti-SARS-CoV-2 71281-22	This paper	GenBank: OR487015, OR487016
Monoclonal anti-SARS-CoV-2 71281-26	This paper	GenBank: OR487023, OR487024
Monoclonal anti-SARS-CoV-2 71281-31	This paper	GenBank: OR487033, OR487034
Monoclonal anti-SARS-CoV-2 71281-32	This paper	GenBank: OR487035, OR487036
Monoclonal anti-SARS-CoV-2 71281-33	This paper	GenBank: OR487037, OR487038
Monoclonal anti-SARS-CoV-2 71281-35	This paper	GenBank: OR487041, OR487042
Monoclonal anti-SARS-CoV-2 71281-36	This paper	GenBank: OR487043, OR487044
Monoclonal anti-SARS-CoV-2 71281-37	This paper	GenBank: OR487045, OR487046
Monoclonal anti-SARS-CoV-2 71282-4	This paper	GenBank: OR487057, OR487058
Monoclonal anti-SARS-CoV-2 71282-6	This paper	GenBank: OR487061, OR487062
Monoclonal anti-SARS-CoV-2 71282-7	This paper	GenBank: OR487063, OR487064
Monoclonal anti-SARS-CoV-2 71282-10	This paper	GenBank: OR487069, OR487070
Monoclonal anti-SARS-CoV-2 71282-14	This paper	GenBank: OR487077, OR487078
Monoclonal anti-SARS-CoV-2 71282-18	This paper	GenBank: OR487085, OR487086
LY-CoV1404	Westendorf et al.⁵⁴	N/A
REGN10987	Copin et al.⁵⁹	N/A
2–7	Liu et al.²²	N/A
CR3022	Yuan et al.⁵⁵	N/A
CB6	Shi et al.²⁵	N/A
DENV-2D22	James Crowe Jr.	N/A

Bacterial and virus strains

VSV-SARS-CoV-2	Case et al.⁴⁴	N/A
VSV-SARS-CoV	This paper	N/A
SARS-CoV-2 D614G pseudotyped lentivirus	Sheward et al.³⁴	N/A
SARS-CoV-2 BA.2 pseudotyped lentivirus	Daniel Sheward	N/A
SARS-CoV-2 BA.5 pseudotyped lentivirus	Sheward et al.³⁴	N/A
SARS-CoV-2 BA.4.6 pseudotyped lentivirus	Sheward et al.³⁴	N/A
SARS-CoV-2 BA.2.75.2 pseudotyped lentivirus	Sheward et al.³⁴	N/A
SARS-CoV-2 XBB pseudotyped lentivirus	Daniel Sheward	N/A
SARS-CoV-2 BQ.1.1 pseudotyped lentivirus	Daniel Sheward	N/A
SARS-CoV-2 XBB.1.5 pseudotyped lentivirus	Daniel Sheward	N/A
SARS-CoV-2 BA.2.75 + R346T pseudotyped lentivirus	This paper	N/A

Biological samples

PBMCs from donors	Mary Arildsen	N/A

Chemicals, peptides, and recombinant proteins

Ghost dye red 780	Tonbo biosciences	Cat#13-0865
Live/Dead fixable aqua dead cell stain kit	Thermo Fisher Scientific	Cat#L34957
Streptavidin HRP	Thermo Fisher Scientific	Cat#ENN100
Polyethyleniminine Linear MW 25000	Polysciences	Cat#23966-1
1-Step Ultra TMB-ELISA Substrate Solution	Thermo Fisher Scientific	Cat#34029
ACE2 with mouse Fc	Sino Biological	Cat#10108-H05H-100
Streptavidin R-phycoerythrin (SA-PE)	Invitrogen	Cat#S866
Galanthus nivalis lectin	Vector Laboratories	Cat#AL-1243-5
Protein A resin	GenScript	Cat#L00210
SARS-CoV-2 S1	Sino Biological	Cat#40591-V08H
SARS-CoV-2 S2	Sino Biological	Cat#40590-V08B
SARS-CoV-2 RBD	Sino Biological	Cat#40592-VNAH
SARS-CoV-2 NTD	Sino Biological	Cat#40591-V49H
HCoV-229E S	Sino Biological	Cat#40605-V08B
HCoV-NL63 S	Sino Biological	Cat#40604-V08B
SARS-CoV-2 S (Hexapro)	PMID: 32703906	N/A
SARS-CoV S (S-2P)	PMID: 28807998	N/A
HCoV-OC43 S (S-2P)	McLellan Lab	N/A
HCoV-HKU1 S (S-2P)	PMID: 28807998	N/A
MERS-CoV S (S-2P)	PMID: 28807998	N/A
A/New Caledonia/20/99 (H1N1)	Barney Graham	GenBank: ACF41878
BG505.N332T.SOSIP.664 gp140 trimer	Ivelin Georgiev	N/A
SARS-CoV-2 S (Hexapro Alpha)	This paper	N/A
SARS-CoV-2 S (Hexapro Beta)	This paper	N/A
SARS-CoV-2 S (Hexapro Delta)	This paper	N/A
SARS-CoV-2 S (Hexapro Omicron BA.1)	This paper	N/A
SARS-CoV-2 S (Hexapro Omicron BA.2)	This paper	N/A
SARS-CoV-2 S (Omicron BA.4/5)	Sino Biological	Cat#40589-V08H32
LYRa11 S (S-2P)	This paper	N/A
RaTG13 S (S-2P)	This paper	N/A
Civet-007-2004 S (S-2P)	This paper	N/A

Critical commercial assays

EZ link Sulfo-NHS-LC-biotin	Thermo Fisher Scientific	Cat#21327
Solulink protein-oligonucleotide conjugation kit	TriLink Biotechnologies	Cat#S-9011
B cell Single Cell V(D)J solution	10X Genomics	N/A
ExpiFectamine™ 293 Transfection Kit	Thermo Fisher Scientific	Cat#A14526
StrepTrap XT prepacked chromatography column	Cytiva	Cat#29401322

Deposited data

71281 heavy and light chain sequences	This paper	GenBank: OR486973-OR487050
71282 heavy and light chain sequences	This paper	GenBank: OR487051-OR487090
Raw next-generation sequencing data	This paper	SRA: PRJNA1014462
71281-33 Fab nsEM map data	This paper	EMDB: EMD-41075, EMD-41076

Experimental models: Cell lines

Human: Expi293F cells	Thermo Fisher Scientific	Cat#A14527
ExpiCHO cells	Thermo Fisher Scientific	Cat#A29127
Vero E6 cells	ATCC	Cat#CRL-1586
HEK-293T-hACE2 cells	BEI	Cat#NR-52511
HEK-293T/17 cells	ATCC	Cat#CRL-11268
HEK-293T cells	ATCC	Cat#CRL-3216

Oligonucleotides

Oligonucleotides for protein DNA-barcoding	Setliff et al.⁴³	N/A

Software and algorithms

Flowjo v10	TreeStar	https://www.flowjo.com/
GraphPad Prism 9.5.0	https://www.graphpad.com:443/	N/A
Cell Ranger	10X Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
HighV-Quest	Alamyar et al.⁶⁰	http://www.imgt.org/IMGTindex/IMGTHighVQUEST.php
ChangeO	Gupta et al.⁶¹	https://changeo.readthedocs.io/en/stable/
cryoSPARC	Punjani et al.⁶²	https://cryosparc.com/updates
ChimeraX	Petterson et al.⁶³	https://www.cgl.ucsf.edu/chimerax/download.html