Major Resources Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-human CD14, APC-eFluor780, clone 61D3 | Thermo Fisher Scientific | Cat#47-0149-42; RRID:AB_1834358 |
| Anti-human CD16, APC-eFluor780, clone eBioCB16 (CB16) | Thermo Fisher Scientific | Cat#47-0168-41; RRID:AB_11219083 |
| Anti-human CD20, PE-Cy7, clone L27 (IVD) | BD Biosciences | Cat#335828; RRID:AB_2868689 |
| Anti-human CD3, APC-eFluor780, clone OKT3 | Thermo Fisher Scientific | Cat#47-0037-41; RRID:AB_2573935 |
| Anti-human CD8a, APC-eFluor780, clone OKT8 | Thermo Fisher Scientific | Cat#47-0086-42; RRID:AB_2573945 |
| Anti-human IgG, HRP-linked whole Ab | GE Healthcare | Cat# NA933; RRID:AB_772208 |
| mAb aCCL8.001 | This paper | n/a |
| mAb aCCL8.003 | This paper | n/a |
| mAb aCCL8.004 | This paper | n/a |
| mAb aCCL8.005 | This paper | n/a |
| mAb aCCL20.001 | This paper | n/a |
| mAb aCXCL13.001 | This paper | n/a |
| mAb aCXCL13.002 | This paper | n/a |
| mAb aCXCL13.003 | This paper | n/a |
| mAb aCXCL16.001 | This paper | n/a |
| mAb aCXCL16.002 | This paper | n/a |
| mAb aCXCL16.003 | This paper | n/a |
| mAb Z021 | Robbiani et al., 2017 | n/a |
| Bacterial and virus strains | ||
| One Shot™ TOP10 Chemically Competent E. coli | Thermo Fisher Scientific | Cat#C404006 |
| Biological samples | ||
| Blood Specimens of SARS-CoV-2 infected or convalescent individuals | Clinica Luganese Moncucco (CLM) | n/a |
| Blood Specimens of SARS-CoV-2 unexposed individuals or from pre-pandemic blood bank donors | Institute for Research in Biomedicine (IRB) | n/a |
| Plasma Specimens of COVID-19-vaccinated individuals | CLM; IRB | n/a |
| Plasma Specimens of HIV-1-infected individuals | Cecchinato et al., 2017 | n/a |
| Plasma Specimens of individuals with AS or RA | University of Zurich (UZH) | n/a |
| Plasma Specimens of individuals with SjS | IRCCS San Matteo | n/a |
| Blood Specimens from buffy coats | Swiss Red Cross | n/a |
| Chemicals, peptides, and recombinant proteins | ||
| Human CCL2 | Clark-Lewis et al., 1997 | n/a |
| Human CCL7 | Clark-Lewis et al., 1997 | n/a |
| Human CCL8 | Peprotech or this paper | Cat#300-15 or n/a |
| Human CCL20 | Clark-Lewis et al., 1997 | n/a |
| Human CXCL13 | Clark-Lewis et al., 1997 | n/a |
| Human CXCL16 | Peprotech | Cat#300-55 |
| NeutrAvidin protein | Thermo Fisher Scientific | Cat#3100 |
| Streptavidin-Alexa Fluor-647 | BioLegend | Cat#405237 |
| Streptavidin-BV711 | BD Biosciences | Cat#563262 |
| Streptavidin-PE | Thermo Fisher Scientific | Cat#12-4317-87 |
| Albumin from chicken egg white | Sigma-Aldrich | Cat#A5503 |
| SARS-CoV-2 RBD | This paper | n/a |
| Synthetic biotinylated peptides (see Table S2) | GenScript (Hong Kong) | https://www.genscript.com/ |
| Critical commercial assays | ||
| EZ-Link™ Sulfo-NHS-LC-Biotinylation Kit | Thermo Fisher Scientific | Cat#21435 |
| Pan B-cell Isolation kit (human) | Milteny Biotech | Cat#130-101-638 |
| CD14 MicroBeads (human) | Milteny Biotech | Cat#130-050-201 |
| CD19 MicroBeads (human) | Milteny Biotech | Cat#130-050-301 |
| Pierce™ TMB Substrate Kit | Thermo Fisher Scientific | Cat#34021 |
| Zombie NIR™ Fixable Viability Kit | BioLegend | Cat#423105 |
| Experimental models: Cell lines | ||
| 293TACE2 | Robbiani et al., 2020 | n/a |
| HEK293T (ATCC CRL-11268) | Robbiani et al., 2020 | n/a |
| Expi293F | Thermo Fisher Scientific | Cat#A14527 |
| PreB 300.19 murine cell line expressing hCCR2 | Ogilvie et al., 2001 | n/a |
| PreB 300.19 murine cell line expressing hCCR6 | Loetscher et al., 1997 | n/a |
| PreB 300.19 murine cell line expressing hCXCR6 | Loetscher et al., 1997 | n/a |
| Oligonucleotides | ||
| Oligonucleotides for antibody cloning | Robbiani et el., 2020 | n/a |
| Recombinant DNA | ||
| pCRV1-NLGagPol (pHIV-1 NLGagPol) | Schmidt et al., 2020 | n/a |
| pNanoLuc2AGFP (pCCNG/nLuc) | Schmidt et al., 2020 | n/a |
| pSARS-CoV-2 (2d19) | Schmidt et al., 2020 | n/a |
| Human IgG1 heavy-chain vector | Robbiani et al., 2020 | n/a |
| Human lambda light-chain vector | Robbiani et al., 2020 | n/a |
| Human kappa light-chain vector | Robbiani et al., 2020 | n/a |
| Software and algorithms | ||
| Adobe Illustrator 2021 | Adobe | https://www.adobe.com/ |
| FlowJo Software (version 10.7.1) | Three Star | https://www.flowjo.com/ |
| Gen5 Software | Agilent | https://www.agilent.com/ |
| Glomax software | Promega | https://www.promega.com/ |
| IgPipeline | Robbiani et al., 2020 | https://www.github.com/stratust/igpipeline |
| Microsoft Excel | Microsoft Excel | https://www.microsoft.com/en-gb/ |
| Prism 9 (version 9.0.2) | GraphPad Software | https://www.graphpad.com/scientificsoftware/prism/ |
| Pretty Heatmaps (pheatmap) R package v 1.0.12 | https://cran.r-project.org/web/packages/pheatmap/index.html | n/a |
| PyMOL 2.5.0 | Schrödinger, Inc. | https://pymol.org |
| Rtsne R package v 0.15 | https://cran.rproject.org/web/packages/Rtsne/ | n/a |
| SnapGene 5.3.2 | SnapGene | https://www.snapgene.com |
| R 4.1.1 | R Development Core Team | https://www.r-project.org/ |
| RStudio 2021.09.0 | RStudio | https://www.rstudio.com/ |
| Other | ||
| Dimethyl sulfoxide | Sigma-Aldrich | Cat#41640 |
| Histopaque | Sigma-Aldrich | Cat#H8889 |
| Medium Expi293 Expression | Thermo Fisher Scientific | Cat#A1435102 |
| Medium GIBCO FreeStyle 293 Expression | Thermo Fisher Scientific | Cat#12338026 |
| Pasteurized Plasma Protein Solution | Swiss Red Cross Laboratory | n/a |
| Polyethylenimine Max PEI-MAX | Polysciences | Cat#24765-1 |
| Protein G Sepharose™ 4 Fast Flow | Cytiva | Cat#17-0618-01P |
| RNasin Ribonuclease Inhibitors | Promega | Cat#N2615 |
| RPMI 1640 Medium, Hepes, no glutamine | Thermo Fisher Scientific | Cat#42401018 |